
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/ACC-TP/6156350/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/6154371/ACC-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=ACC-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=ACC-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/ACC-TP/6154371/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/6156350/transformed.cor.cli.txt"

nPatients in clinical file=10, in cluster file=90, common to both=10
[1] "Reduce the number of clustering variables from 45 to 27."
[1] 27 10
[1] "AMP PEAK  2(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                            5                             5 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                            5                             5 
[1] "AMP PEAK  3(4Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                            4                             6 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                            4                             6 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             6                              4 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             6                              4 
[1] "AMP PEAK  5(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            5                             5 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            5                             5 
[1] "AMP PEAK  8(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                            4                             6 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                            4                             6 
[1] "AMP PEAK 10(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                             7                              3 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                             7                              3 
[1] "AMP PEAK 11(14Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                             4                              6 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                             4                              6 
[1] "AMP PEAK 12(16P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                             5                              5 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                             5                              5 
[1] "AMP PEAK 13(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                             5                              5 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                             5                              5 
[1] "AMP PEAK 14(16Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                             5                              5 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                             5                              5 
[1] "AMP PEAK 16(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                              7                               3 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                              7                               3 
[1] "AMP PEAK 17(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                           7                            3 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                           7                            3 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             7                              3 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             7                              3 
[1] "DEL PEAK  2(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          3                           7 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          3                           7 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            4                             6 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            4                             6 
[1] "DEL PEAK  7(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                            3                             7 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                            3                             7 
[1] "DEL PEAK 10(7Q32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            3                             7 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            3                             7 
[1] "DEL PEAK 12(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                            4                             6 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                            4                             6 
[1] "DEL PEAK 14(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                             5                              5 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                             5                              5 
[1] "DEL PEAK 15(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                             5                              5 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                             5                              5 
[1] "DEL PEAK 17(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                             5                              5 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                             5                              5 
[1] "DEL PEAK 21(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                             4                              6 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                             4                              6 
[1] "DEL PEAK 22(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                              3                               7 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                              3                               7 
[1] "DEL PEAK 23(17Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                             5                              5 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                             5                              5 
[1] "DEL PEAK 24(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                             5                              5 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                             5                              5 
[1] "DEL PEAK 25(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             3                              7 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             3                              7 
[1] "DEL PEAK 26(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                             6                              4 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                             6                              4 
[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] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "GLEASON_SCORE"                         
[14] "PSA_VALUE"                             
[15] "DAYS_TO_PSA"                           
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 10 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO 
          NA           NA         1423          309           NA          889 
TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
        3688         1130           NA          709 
Variable 1:'AGE':	nDistinctValues=10,	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=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	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:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "GENDER"               
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N"
Output Data has 10 columns, 1 survival variables, and 4 non-survival variables.
AGE, nv=10, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=3, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T4 
 3  3  3 
[1] "table(vv)"
vv
T1+T2+T4 
       9 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T4 
 3  3  3 

$nClasses
[1] 1

$ClinVariableType
[1] "multiclass(1)"


T1+T2+T4 
       9 
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  2(4P16.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  2(4P16.3) MUTATED   4 1
  AMP PEAK  2(4P16.3) WILD-TYPE 2 3
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                            5                             5 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                            1                             3 
$`AMP PEAK  2(4P16.3) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78        10.16       121.25        23.31 

$`AMP PEAK  2(4P16.3) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        29.23        37.15        11.31 

  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                        10.16                         11.31 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                       121.25                         37.15 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                        46.78                         18.08 
[1] "10.2 - 121.2 (46.8)" "11.3 - 37.1 (18.1)" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  2(4P16.3) WILD-TYPE"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  2(4P16.3) MUTATED"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  2(4P16.3) WILD-TYPE" "AMP PEAK  2(4P16.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  2(4P16.3) MUTATED" "AMP PEAK  2(4P16.3) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  2(4P16.3) WILD-TYPE"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  2(4P16.3) WILD-TYPE"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  2(4P16.3) MUTATED"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  2(4P16.3) WILD-TYPE" "AMP PEAK  2(4P16.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  2(4P16.3) MUTATED" "AMP PEAK  2(4P16.3) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  2(4P16.3) WILD-TYPE"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  2(4P16.3) WILD-TYPE"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  2(4P16.3) MUTATED"   "AMP PEAK  2(4P16.3) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  2(4P16.3) WILD-TYPE" "AMP PEAK  2(4P16.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  2(4P16.3) MUTATED" "AMP PEAK  2(4P16.3) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  2(4P16.3) WILD-TYPE"   "AMP PEAK  2(4P16.3) MUTATED" 
[1] "hr="     "1.7e+09"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  AMP PEAK  2(4P16.3) MUTATED         2        0        2
  AMP PEAK  2(4P16.3) WILD-TYPE       1        2        2
D1V3, multiclass
          clus
vv         AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  STAGE I                            2                             1
  STAGE II                           0                             2
  STAGE IV                           2                             2
                               vv
clus                            T1+T2+T4
  AMP PEAK  2(4P16.3) MUTATED          4
  AMP PEAK  2(4P16.3) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D1V5, binary
                               cls
clus                            0 1
  AMP PEAK  2(4P16.3) MUTATED   1 4
  AMP PEAK  2(4P16.3) WILD-TYPE 4 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED      1    4
  AMP PEAK  2(4P16.3) WILD-TYPE    4    1
        clus
vv       AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  FEMALE                           1                             4
  MALE                             4                             1

Clustering(2) Variable = AMP PEAK  3(4Q35.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  3(4Q35.1) MUTATED   3 1
  AMP PEAK  3(4Q35.1) WILD-TYPE 3 3
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                            4                             6 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                            1                             3 
$`AMP PEAK  3(4Q35.1) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78       121.25        23.31 

$`AMP PEAK  3(4Q35.1) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        10.16        18.05        29.23        37.15        11.31 

  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                        23.31                         10.16 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                       121.25                         37.15 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                       52.155                        18.065 
[1] "23.3 - 121.2 (52.2)" "10.2 - 37.1 (18.1)" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  3(4Q35.1) WILD-TYPE"   "AMP PEAK  3(4Q35.1) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  3(4Q35.1) MUTATED" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  3(4Q35.1) WILD-TYPE" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  3(4Q35.1) MUTATED" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  3(4Q35.1) WILD-TYPE"   "AMP PEAK  3(4Q35.1) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  3(4Q35.1) WILD-TYPE"   "AMP PEAK  3(4Q35.1) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  3(4Q35.1) MUTATED" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  3(4Q35.1) WILD-TYPE" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  3(4Q35.1) MUTATED" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  3(4Q35.1) WILD-TYPE"   "AMP PEAK  3(4Q35.1) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  3(4Q35.1) WILD-TYPE"   "AMP PEAK  3(4Q35.1) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  3(4Q35.1) MUTATED" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  3(4Q35.1) WILD-TYPE" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  3(4Q35.1) MUTATED" "AMP PEAK  3(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  3(4Q35.1) WILD-TYPE"   "AMP PEAK  3(4Q35.1) MUTATED" 
[1] "hr="     "1.7e+09"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  AMP PEAK  3(4Q35.1) MUTATED         2        0        1
  AMP PEAK  3(4Q35.1) WILD-TYPE       1        2        3
D2V3, multiclass
          clus
vv         AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  STAGE I                            2                             1
  STAGE II                           0                             2
  STAGE IV                           1                             3
                               vv
clus                            T1+T2+T4
  AMP PEAK  3(4Q35.1) MUTATED          3
  AMP PEAK  3(4Q35.1) WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D2V5, binary
                               cls
clus                            0 1
  AMP PEAK  3(4Q35.1) MUTATED   1 3
  AMP PEAK  3(4Q35.1) WILD-TYPE 4 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(4Q35.1) MUTATED      1    3
  AMP PEAK  3(4Q35.1) WILD-TYPE    4    2
        clus
vv       AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  FEMALE                           1                             4
  MALE                             3                             2

Clustering(3) Variable = AMP PEAK  4(5P15.33) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                            0 1
  AMP PEAK  4(5P15.33) MUTATED   4 2
  AMP PEAK  4(5P15.33) WILD-TYPE 2 2
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             6                              4 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             2                              2 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OR-A5K9 TCGA-OU-A5PI 
       57.53        46.78        10.16       121.25        11.31        23.31 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        18.05        29.23        37.15 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         10.16                          18.05 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        121.25                          37.15 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        35.045                         23.655 
[1] "10.2 - 121.2 (35.0)" "18.1 - 37.1 (23.7)" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
[1] "hr=" "2.4"
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  AMP PEAK  4(5P15.33) MUTATED         2        1        2
  AMP PEAK  4(5P15.33) WILD-TYPE       1        1        2
D3V3, multiclass
          clus
vv         AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  STAGE I                             2                              1
  STAGE II                            1                              1
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  AMP PEAK  4(5P15.33) MUTATED          5
  AMP PEAK  4(5P15.33) WILD-TYPE        4
[1] "NOT AVAILABLE: table dimension [2x1]"
D3V5, binary
                                cls
clus                             0 1
  AMP PEAK  4(5P15.33) MUTATED   2 4
  AMP PEAK  4(5P15.33) WILD-TYPE 3 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      2    4
  AMP PEAK  4(5P15.33) WILD-TYPE    3    1
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                            2                              3
  MALE                              4                              1

Clustering(4) Variable = AMP PEAK  5(5Q35.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  5(5Q35.3) MUTATED   4 1
  AMP PEAK  5(5Q35.3) WILD-TYPE 2 3
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            5                             5 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            1                             3 
$`AMP PEAK  5(5Q35.3) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78        10.16       121.25        23.31 

$`AMP PEAK  5(5Q35.3) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        29.23        37.15        11.31 

  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                        10.16                         11.31 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                       121.25                         37.15 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                        46.78                         18.08 
[1] "10.2 - 121.2 (46.8)" "11.3 - 37.1 (18.1)" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  5(5Q35.3) MUTATED"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  5(5Q35.3) MUTATED"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
  "AMP PEAK  5(5Q35.3) MUTATED"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
[1] "hr="     "1.7e+09"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  AMP PEAK  5(5Q35.3) MUTATED         2        0        2
  AMP PEAK  5(5Q35.3) WILD-TYPE       1        2        2
D4V3, multiclass
          clus
vv         AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  STAGE I                            2                             1
  STAGE II                           0                             2
  STAGE IV                           2                             2
                               vv
clus                            T1+T2+T4
  AMP PEAK  5(5Q35.3) MUTATED          4
  AMP PEAK  5(5Q35.3) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D4V5, binary
                               cls
clus                            0 1
  AMP PEAK  5(5Q35.3) MUTATED   1 4
  AMP PEAK  5(5Q35.3) WILD-TYPE 4 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      1    4
  AMP PEAK  5(5Q35.3) WILD-TYPE    4    1
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  FEMALE                           1                             4
  MALE                             4                             1

Clustering(5) Variable = AMP PEAK  8(7P22.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  8(7P22.1) MUTATED   4 0
  AMP PEAK  8(7P22.1) WILD-TYPE 2 4
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                            4                             6 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                            0                             4 
$`AMP PEAK  8(7P22.1) MUTATED`
TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OU-A5PI 
       10.16       121.25        37.15        23.31 

$`AMP PEAK  8(7P22.1) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K9 
       18.08        57.53        46.78        18.05        29.23        11.31 

  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                        10.16                         11.31 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                       121.25                         57.53 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                       30.230                        23.655 
[1] "10.2 - 121.2 (30.2)" "11.3 - 57.5 (23.7)" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
[1] "hr="     "1.2e+09"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  AMP PEAK  8(7P22.1) MUTATED         1        1        2
  AMP PEAK  8(7P22.1) WILD-TYPE       2        1        2
D5V3, multiclass
          clus
vv         AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  STAGE I                            1                             2
  STAGE II                           1                             1
  STAGE IV                           2                             2
                               vv
clus                            T1+T2+T4
  AMP PEAK  8(7P22.1) MUTATED          4
  AMP PEAK  8(7P22.1) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D5V5, binary
                               cls
clus                            0 1
  AMP PEAK  8(7P22.1) MUTATED   2 2
  AMP PEAK  8(7P22.1) WILD-TYPE 3 3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED      2    2
  AMP PEAK  8(7P22.1) WILD-TYPE    3    3
        clus
vv       AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  FEMALE                           2                             3
  MALE                             2                             3

Clustering(6) Variable = AMP PEAK 10(12Q14.1) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 10(12Q14.1) MUTATED   4 3
  AMP PEAK 10(12Q14.1) WILD-TYPE 2 1
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                             7                              3 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                             3                              1 
$`AMP PEAK 10(12Q14.1) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JR TCGA-OR-A5K9 
       57.53        46.78        10.16        18.05       121.25        11.31 
TCGA-OU-A5PI 
       23.31 

$`AMP PEAK 10(12Q14.1) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        29.23        37.15 

  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                         10.16                          18.08 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                        121.25                          37.15 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                         23.31                          29.23 
[1] "10.2 - 121.2 (23.3)" "18.1 - 37.1 (29.2)" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 10(12Q14.1) WILD-TYPE"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 10(12Q14.1) MUTATED"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "AMP PEAK 10(12Q14.1) MUTATED" "AMP PEAK 10(12Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 10(12Q14.1) MUTATED" "AMP PEAK 10(12Q14.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "AMP PEAK 10(12Q14.1) MUTATED"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 10(12Q14.1) WILD-TYPE"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 10(12Q14.1) MUTATED"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "AMP PEAK 10(12Q14.1) MUTATED" "AMP PEAK 10(12Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 10(12Q14.1) MUTATED" "AMP PEAK 10(12Q14.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "AMP PEAK 10(12Q14.1) MUTATED"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 10(12Q14.1) WILD-TYPE"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 10(12Q14.1) MUTATED"   "AMP PEAK 10(12Q14.1) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "AMP PEAK 10(12Q14.1) MUTATED" "AMP PEAK 10(12Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 10(12Q14.1) MUTATED" "AMP PEAK 10(12Q14.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "AMP PEAK 10(12Q14.1) MUTATED"   "AMP PEAK 10(12Q14.1) MUTATED" 
[1] "hr=" "1.2"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  AMP PEAK 10(12Q14.1) MUTATED         2        1        3
  AMP PEAK 10(12Q14.1) WILD-TYPE       1        1        1
D6V3, multiclass
          clus
vv         AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  STAGE I                             2                              1
  STAGE II                            1                              1
  STAGE IV                            3                              1
                                vv
clus                             T1+T2+T4
  AMP PEAK 10(12Q14.1) MUTATED          6
  AMP PEAK 10(12Q14.1) WILD-TYPE        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D6V5, binary
                                cls
clus                             0 1
  AMP PEAK 10(12Q14.1) MUTATED   3 4
  AMP PEAK 10(12Q14.1) WILD-TYPE 2 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12Q14.1) MUTATED      3    4
  AMP PEAK 10(12Q14.1) WILD-TYPE    2    1
        clus
vv       AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  FEMALE                            3                              2
  MALE                              4                              1

Clustering(7) Variable = AMP PEAK 11(14Q11.2) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 11(14Q11.2) MUTATED   2 2
  AMP PEAK 11(14Q11.2) WILD-TYPE 4 2
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                             4                              6 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                             2                              2 
$`AMP PEAK 11(14Q11.2) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OU-A5PI 
       57.53        10.16        18.05        23.31 

$`AMP PEAK 11(14Q11.2) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        46.78        29.23       121.25        37.15        11.31 

  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                         10.16                          11.31 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                         57.53                         121.25 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                         20.68                          33.19 
[1] "10.2 - 57.5 (20.7)"  "11.3 - 121.2 (33.2)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "AMP PEAK 11(14Q11.2) MUTATED" "AMP PEAK 11(14Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"AMP PEAK 11(14Q11.2) WILD-TYPE" "AMP PEAK 11(14Q11.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "AMP PEAK 11(14Q11.2) MUTATED" "AMP PEAK 11(14Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"AMP PEAK 11(14Q11.2) WILD-TYPE" "AMP PEAK 11(14Q11.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "AMP PEAK 11(14Q11.2) MUTATED" "AMP PEAK 11(14Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"AMP PEAK 11(14Q11.2) WILD-TYPE" "AMP PEAK 11(14Q11.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 11(14Q11.2) WILD-TYPE"   "AMP PEAK 11(14Q11.2) MUTATED" 
[1] "hr=" "1.7"
D7V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  AMP PEAK 11(14Q11.2) MUTATED         0        0        3
  AMP PEAK 11(14Q11.2) WILD-TYPE       3        2        1
D7V3, multiclass
          clus
vv         AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  STAGE I                             0                              3
  STAGE II                            0                              2
  STAGE IV                            3                              1
                                vv
clus                             T1+T2+T4
  AMP PEAK 11(14Q11.2) MUTATED          3
  AMP PEAK 11(14Q11.2) WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D7V5, binary
                                cls
clus                             0 1
  AMP PEAK 11(14Q11.2) MUTATED   2 2
  AMP PEAK 11(14Q11.2) WILD-TYPE 3 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(14Q11.2) MUTATED      2    2
  AMP PEAK 11(14Q11.2) WILD-TYPE    3    3
        clus
vv       AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  FEMALE                            2                              3
  MALE                              2                              3

Clustering(8) Variable = AMP PEAK 12(16P13.3) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 12(16P13.3) MUTATED   4 1
  AMP PEAK 12(16P13.3) WILD-TYPE 2 3
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                             5                              5 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                             1                              3 
$`AMP PEAK 12(16P13.3) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78        10.16       121.25        23.31 

$`AMP PEAK 12(16P13.3) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        29.23        37.15        11.31 

  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                         10.16                          11.31 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                        121.25                          37.15 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                         46.78                          18.08 
[1] "10.2 - 121.2 (46.8)" "11.3 - 37.1 (18.1)" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 12(16P13.3) WILD-TYPE"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 12(16P13.3) MUTATED"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 12(16P13.3) WILD-TYPE" "AMP PEAK 12(16P13.3) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 12(16P13.3) MUTATED" "AMP PEAK 12(16P13.3) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 12(16P13.3) WILD-TYPE"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 12(16P13.3) WILD-TYPE"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 12(16P13.3) MUTATED"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 12(16P13.3) WILD-TYPE" "AMP PEAK 12(16P13.3) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 12(16P13.3) MUTATED" "AMP PEAK 12(16P13.3) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 12(16P13.3) WILD-TYPE"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 12(16P13.3) WILD-TYPE"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 12(16P13.3) MUTATED"   "AMP PEAK 12(16P13.3) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 12(16P13.3) WILD-TYPE" "AMP PEAK 12(16P13.3) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 12(16P13.3) MUTATED" "AMP PEAK 12(16P13.3) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 12(16P13.3) WILD-TYPE"   "AMP PEAK 12(16P13.3) MUTATED" 
[1] "hr="     "1.7e+09"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  AMP PEAK 12(16P13.3) MUTATED         2        0        2
  AMP PEAK 12(16P13.3) WILD-TYPE       1        2        2
D8V3, multiclass
          clus
vv         AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  STAGE I                             2                              1
  STAGE II                            0                              2
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  AMP PEAK 12(16P13.3) MUTATED          4
  AMP PEAK 12(16P13.3) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D8V5, binary
                                cls
clus                             0 1
  AMP PEAK 12(16P13.3) MUTATED   1 4
  AMP PEAK 12(16P13.3) WILD-TYPE 4 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16P13.3) MUTATED      1    4
  AMP PEAK 12(16P13.3) WILD-TYPE    4    1
        clus
vv       AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  FEMALE                            1                              4
  MALE                              4                              1

Clustering(9) Variable = AMP PEAK 13(16Q22.1) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 13(16Q22.1) MUTATED   4 1
  AMP PEAK 13(16Q22.1) WILD-TYPE 2 3
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                             5                              5 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                             1                              3 
$`AMP PEAK 13(16Q22.1) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78        10.16       121.25        23.31 

$`AMP PEAK 13(16Q22.1) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        29.23        37.15        11.31 

  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                         10.16                          11.31 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                        121.25                          37.15 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                         46.78                          18.08 
[1] "10.2 - 121.2 (46.8)" "11.3 - 37.1 (18.1)" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 13(16Q22.1) WILD-TYPE"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 13(16Q22.1) MUTATED"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 13(16Q22.1) WILD-TYPE" "AMP PEAK 13(16Q22.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 13(16Q22.1) MUTATED" "AMP PEAK 13(16Q22.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 13(16Q22.1) WILD-TYPE"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 13(16Q22.1) WILD-TYPE"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 13(16Q22.1) MUTATED"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 13(16Q22.1) WILD-TYPE" "AMP PEAK 13(16Q22.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 13(16Q22.1) MUTATED" "AMP PEAK 13(16Q22.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 13(16Q22.1) WILD-TYPE"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 13(16Q22.1) WILD-TYPE"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 13(16Q22.1) MUTATED"   "AMP PEAK 13(16Q22.1) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 13(16Q22.1) WILD-TYPE" "AMP PEAK 13(16Q22.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 13(16Q22.1) MUTATED" "AMP PEAK 13(16Q22.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 13(16Q22.1) WILD-TYPE"   "AMP PEAK 13(16Q22.1) MUTATED" 
[1] "hr="     "1.7e+09"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  AMP PEAK 13(16Q22.1) MUTATED         2        0        2
  AMP PEAK 13(16Q22.1) WILD-TYPE       1        2        2
D9V3, multiclass
          clus
vv         AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  STAGE I                             2                              1
  STAGE II                            0                              2
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  AMP PEAK 13(16Q22.1) MUTATED          4
  AMP PEAK 13(16Q22.1) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D9V5, binary
                                cls
clus                             0 1
  AMP PEAK 13(16Q22.1) MUTATED   1 4
  AMP PEAK 13(16Q22.1) WILD-TYPE 4 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q22.1) MUTATED      1    4
  AMP PEAK 13(16Q22.1) WILD-TYPE    4    1
        clus
vv       AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  FEMALE                            1                              4
  MALE                              4                              1

Clustering(10) Variable = AMP PEAK 14(16Q24.2) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 14(16Q24.2) MUTATED   4 1
  AMP PEAK 14(16Q24.2) WILD-TYPE 2 3
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                             5                              5 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                             1                              3 
$`AMP PEAK 14(16Q24.2) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78        10.16       121.25        23.31 

$`AMP PEAK 14(16Q24.2) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        29.23        37.15        11.31 

  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                         10.16                          11.31 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                        121.25                          37.15 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                         46.78                          18.08 
[1] "10.2 - 121.2 (46.8)" "11.3 - 37.1 (18.1)" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 14(16Q24.2) WILD-TYPE"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 14(16Q24.2) MUTATED"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 14(16Q24.2) WILD-TYPE" "AMP PEAK 14(16Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 14(16Q24.2) MUTATED" "AMP PEAK 14(16Q24.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 14(16Q24.2) WILD-TYPE"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 14(16Q24.2) WILD-TYPE"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 14(16Q24.2) MUTATED"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 14(16Q24.2) WILD-TYPE" "AMP PEAK 14(16Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 14(16Q24.2) MUTATED" "AMP PEAK 14(16Q24.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 14(16Q24.2) WILD-TYPE"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"AMP PEAK 14(16Q24.2) WILD-TYPE"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "AMP PEAK 14(16Q24.2) MUTATED"   "AMP PEAK 14(16Q24.2) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"AMP PEAK 14(16Q24.2) WILD-TYPE" "AMP PEAK 14(16Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "AMP PEAK 14(16Q24.2) MUTATED" "AMP PEAK 14(16Q24.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"AMP PEAK 14(16Q24.2) WILD-TYPE"   "AMP PEAK 14(16Q24.2) MUTATED" 
[1] "hr="     "1.7e+09"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  AMP PEAK 14(16Q24.2) MUTATED         2        0        2
  AMP PEAK 14(16Q24.2) WILD-TYPE       1        2        2
D10V3, multiclass
          clus
vv         AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  STAGE I                             2                              1
  STAGE II                            0                              2
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  AMP PEAK 14(16Q24.2) MUTATED          4
  AMP PEAK 14(16Q24.2) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D10V5, binary
                                cls
clus                             0 1
  AMP PEAK 14(16Q24.2) MUTATED   1 4
  AMP PEAK 14(16Q24.2) WILD-TYPE 4 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q24.2) MUTATED      1    4
  AMP PEAK 14(16Q24.2) WILD-TYPE    4    1
        clus
vv       AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  FEMALE                            1                              4
  MALE                              4                              1

Clustering(11) Variable = AMP PEAK 16(19P13.12) MUTATION ANALYSIS
D11V1, survival
                                 sevent
clus2                             0 1
  AMP PEAK 16(19P13.12) MUTATED   4 3
  AMP PEAK 16(19P13.12) WILD-TYPE 2 1
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                              7                               3 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                              3                               1 
$`AMP PEAK 16(19P13.12) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JR TCGA-OR-A5K9 
       57.53        46.78        10.16        18.05       121.25        11.31 
TCGA-OU-A5PI 
       23.31 

$`AMP PEAK 16(19P13.12) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        29.23        37.15 

  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                          10.16                           18.08 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                         121.25                           37.15 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                          23.31                           29.23 
[1] "10.2 - 121.2 (23.3)" "18.1 - 37.1 (29.2)" 
                     TCGA-OR-A5JB                      TCGA-OR-A5JC 
"AMP PEAK 16(19P13.12) WILD-TYPE"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JI                      TCGA-OR-A5JJ 
  "AMP PEAK 16(19P13.12) MUTATED"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JM                      TCGA-OR-A5JO 
  "AMP PEAK 16(19P13.12) MUTATED" "AMP PEAK 16(19P13.12) WILD-TYPE" 
                     TCGA-OR-A5JR                      TCGA-OR-A5K6 
  "AMP PEAK 16(19P13.12) MUTATED" "AMP PEAK 16(19P13.12) WILD-TYPE" 
                     TCGA-OR-A5K9                      TCGA-OU-A5PI 
  "AMP PEAK 16(19P13.12) MUTATED"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JB                      TCGA-OR-A5JC 
"AMP PEAK 16(19P13.12) WILD-TYPE"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JI                      TCGA-OR-A5JJ 
  "AMP PEAK 16(19P13.12) MUTATED"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JM                      TCGA-OR-A5JO 
  "AMP PEAK 16(19P13.12) MUTATED" "AMP PEAK 16(19P13.12) WILD-TYPE" 
                     TCGA-OR-A5JR                      TCGA-OR-A5K6 
  "AMP PEAK 16(19P13.12) MUTATED" "AMP PEAK 16(19P13.12) WILD-TYPE" 
                     TCGA-OR-A5K9                      TCGA-OU-A5PI 
  "AMP PEAK 16(19P13.12) MUTATED"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JB                      TCGA-OR-A5JC 
"AMP PEAK 16(19P13.12) WILD-TYPE"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JI                      TCGA-OR-A5JJ 
  "AMP PEAK 16(19P13.12) MUTATED"   "AMP PEAK 16(19P13.12) MUTATED" 
                     TCGA-OR-A5JM                      TCGA-OR-A5JO 
  "AMP PEAK 16(19P13.12) MUTATED" "AMP PEAK 16(19P13.12) WILD-TYPE" 
                     TCGA-OR-A5JR                      TCGA-OR-A5K6 
  "AMP PEAK 16(19P13.12) MUTATED" "AMP PEAK 16(19P13.12) WILD-TYPE" 
                     TCGA-OR-A5K9                      TCGA-OU-A5PI 
  "AMP PEAK 16(19P13.12) MUTATED"   "AMP PEAK 16(19P13.12) MUTATED" 
[1] "hr=" "1.2"
D11V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IV
  AMP PEAK 16(19P13.12) MUTATED         2        1        3
  AMP PEAK 16(19P13.12) WILD-TYPE       1        1        1
D11V3, multiclass
          clus
vv         AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  STAGE I                              2                               1
  STAGE II                             1                               1
  STAGE IV                             3                               1
                                 vv
clus                              T1+T2+T4
  AMP PEAK 16(19P13.12) MUTATED          6
  AMP PEAK 16(19P13.12) WILD-TYPE        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D11V5, binary
                                 cls
clus                              0 1
  AMP PEAK 16(19P13.12) MUTATED   3 4
  AMP PEAK 16(19P13.12) WILD-TYPE 2 1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19P13.12) MUTATED      3    4
  AMP PEAK 16(19P13.12) WILD-TYPE    2    1
        clus
vv       AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  FEMALE                             3                               2
  MALE                               4                               1

Clustering(12) Variable = AMP PEAK 17(19Q12) MUTATION ANALYSIS
D12V1, survival
                              sevent
clus2                          0 1
  AMP PEAK 17(19Q12) MUTATED   4 3
  AMP PEAK 17(19Q12) WILD-TYPE 2 1
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                           7                            3 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                           3                            1 
$`AMP PEAK 17(19Q12) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JR TCGA-OR-A5K9 
       57.53        46.78        10.16        18.05       121.25        11.31 
TCGA-OU-A5PI 
       23.31 

$`AMP PEAK 17(19Q12) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        29.23        37.15 

  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                       10.16                        18.08 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                      121.25                        37.15 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                       23.31                        29.23 
[1] "10.2 - 121.2 (23.3)" "18.1 - 37.1 (29.2)" 
                  TCGA-OR-A5JB                   TCGA-OR-A5JC 
"AMP PEAK 17(19Q12) WILD-TYPE"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JI                   TCGA-OR-A5JJ 
  "AMP PEAK 17(19Q12) MUTATED"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JM                   TCGA-OR-A5JO 
  "AMP PEAK 17(19Q12) MUTATED" "AMP PEAK 17(19Q12) WILD-TYPE" 
                  TCGA-OR-A5JR                   TCGA-OR-A5K6 
  "AMP PEAK 17(19Q12) MUTATED" "AMP PEAK 17(19Q12) WILD-TYPE" 
                  TCGA-OR-A5K9                   TCGA-OU-A5PI 
  "AMP PEAK 17(19Q12) MUTATED"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JB                   TCGA-OR-A5JC 
"AMP PEAK 17(19Q12) WILD-TYPE"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JI                   TCGA-OR-A5JJ 
  "AMP PEAK 17(19Q12) MUTATED"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JM                   TCGA-OR-A5JO 
  "AMP PEAK 17(19Q12) MUTATED" "AMP PEAK 17(19Q12) WILD-TYPE" 
                  TCGA-OR-A5JR                   TCGA-OR-A5K6 
  "AMP PEAK 17(19Q12) MUTATED" "AMP PEAK 17(19Q12) WILD-TYPE" 
                  TCGA-OR-A5K9                   TCGA-OU-A5PI 
  "AMP PEAK 17(19Q12) MUTATED"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JB                   TCGA-OR-A5JC 
"AMP PEAK 17(19Q12) WILD-TYPE"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JI                   TCGA-OR-A5JJ 
  "AMP PEAK 17(19Q12) MUTATED"   "AMP PEAK 17(19Q12) MUTATED" 
                  TCGA-OR-A5JM                   TCGA-OR-A5JO 
  "AMP PEAK 17(19Q12) MUTATED" "AMP PEAK 17(19Q12) WILD-TYPE" 
                  TCGA-OR-A5JR                   TCGA-OR-A5K6 
  "AMP PEAK 17(19Q12) MUTATED" "AMP PEAK 17(19Q12) WILD-TYPE" 
                  TCGA-OR-A5K9                   TCGA-OU-A5PI 
  "AMP PEAK 17(19Q12) MUTATED"   "AMP PEAK 17(19Q12) MUTATED" 
[1] "hr=" "1.2"
D12V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE IV
  AMP PEAK 17(19Q12) MUTATED         2        1        3
  AMP PEAK 17(19Q12) WILD-TYPE       1        1        1
D12V3, multiclass
          clus
vv         AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  STAGE I                           2                            1
  STAGE II                          1                            1
  STAGE IV                          3                            1
                              vv
clus                           T1+T2+T4
  AMP PEAK 17(19Q12) MUTATED          6
  AMP PEAK 17(19Q12) WILD-TYPE        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D12V5, binary
                              cls
clus                           0 1
  AMP PEAK 17(19Q12) MUTATED   3 4
  AMP PEAK 17(19Q12) WILD-TYPE 2 1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED      3    4
  AMP PEAK 17(19Q12) WILD-TYPE    2    1
        clus
vv       AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  FEMALE                          3                            2
  MALE                            4                            1

Clustering(13) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                            0 1
  DEL PEAK  1(1P36.23) MUTATED   4 3
  DEL PEAK  1(1P36.23) WILD-TYPE 2 1
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             7                              3 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             3                              1 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OR-A5K9 
       57.53        46.78        10.16        18.05        37.15        11.31 
TCGA-OU-A5PI 
       23.31 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5JR 
       18.08        29.23       121.25 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         10.16                          18.08 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         57.53                         121.25 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         23.31                          29.23 
[1] "10.2 - 57.5 (23.3)"  "18.1 - 121.2 (29.2)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK  1(1P36.23) WILD-TYPE"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK  1(1P36.23) MUTATED"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK  1(1P36.23) MUTATED" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK  1(1P36.23) WILD-TYPE"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK  1(1P36.23) MUTATED"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK  1(1P36.23) WILD-TYPE"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK  1(1P36.23) MUTATED"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK  1(1P36.23) MUTATED" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK  1(1P36.23) WILD-TYPE"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK  1(1P36.23) MUTATED"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK  1(1P36.23) WILD-TYPE"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK  1(1P36.23) MUTATED"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK  1(1P36.23) MUTATED" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK  1(1P36.23) WILD-TYPE"   "DEL PEAK  1(1P36.23) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK  1(1P36.23) MUTATED"   "DEL PEAK  1(1P36.23) MUTATED" 
[1] "hr=" "2.1"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK  1(1P36.23) MUTATED         1        2        3
  DEL PEAK  1(1P36.23) WILD-TYPE       2        0        1
D13V3, multiclass
          clus
vv         DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                             1                              2
  STAGE II                            2                              0
  STAGE IV                            3                              1
                                vv
clus                             T1+T2+T4
  DEL PEAK  1(1P36.23) MUTATED          6
  DEL PEAK  1(1P36.23) WILD-TYPE        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D13V5, binary
                                cls
clus                             0 1
  DEL PEAK  1(1P36.23) MUTATED   4 3
  DEL PEAK  1(1P36.23) WILD-TYPE 1 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      4    3
  DEL PEAK  1(1P36.23) WILD-TYPE    1    2
        clus
vv       DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  FEMALE                            4                              1
  MALE                              3                              2

Clustering(14) Variable = DEL PEAK  2(1Q43) MUTATION ANALYSIS
D14V1, survival
                             sevent
clus2                         0 1
  DEL PEAK  2(1Q43) MUTATED   2 1
  DEL PEAK  2(1Q43) WILD-TYPE 4 3
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          3                           7 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          1                           3 
$`DEL PEAK  2(1Q43) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OU-A5PI 
       57.53        46.78        23.31 

$`DEL PEAK  2(1Q43) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       18.08        10.16        18.05        29.23       121.25        37.15 
TCGA-OR-A5K9 
       11.31 

  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      23.31                       10.16 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      57.53                      121.25 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      46.78                       18.08 
[1] "23.3 - 57.5 (46.8)"  "10.2 - 121.2 (18.1)"
                 TCGA-OR-A5JB                  TCGA-OR-A5JC 
"DEL PEAK  2(1Q43) WILD-TYPE"   "DEL PEAK  2(1Q43) MUTATED" 
                 TCGA-OR-A5JI                  TCGA-OR-A5JJ 
  "DEL PEAK  2(1Q43) MUTATED" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JM                  TCGA-OR-A5JO 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JR                  TCGA-OR-A5K6 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5K9                  TCGA-OU-A5PI 
"DEL PEAK  2(1Q43) WILD-TYPE"   "DEL PEAK  2(1Q43) MUTATED" 
                 TCGA-OR-A5JB                  TCGA-OR-A5JC 
"DEL PEAK  2(1Q43) WILD-TYPE"   "DEL PEAK  2(1Q43) MUTATED" 
                 TCGA-OR-A5JI                  TCGA-OR-A5JJ 
  "DEL PEAK  2(1Q43) MUTATED" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JM                  TCGA-OR-A5JO 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JR                  TCGA-OR-A5K6 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5K9                  TCGA-OU-A5PI 
"DEL PEAK  2(1Q43) WILD-TYPE"   "DEL PEAK  2(1Q43) MUTATED" 
                 TCGA-OR-A5JB                  TCGA-OR-A5JC 
"DEL PEAK  2(1Q43) WILD-TYPE"   "DEL PEAK  2(1Q43) MUTATED" 
                 TCGA-OR-A5JI                  TCGA-OR-A5JJ 
  "DEL PEAK  2(1Q43) MUTATED" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JM                  TCGA-OR-A5JO 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JR                  TCGA-OR-A5K6 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5K9                  TCGA-OU-A5PI 
"DEL PEAK  2(1Q43) WILD-TYPE"   "DEL PEAK  2(1Q43) MUTATED" 
[1] "hr=" "2.1"
D14V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IV
  DEL PEAK  2(1Q43) MUTATED         1        0        1
  DEL PEAK  2(1Q43) WILD-TYPE       2        2        3
D14V3, multiclass
[1] "Remove cluster labels:"    "DEL PEAK  2(1Q43) MUTATED"
clus
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          2                           7 
                 TCGA-OR-A5JB                  TCGA-OR-A5JJ 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JM                  TCGA-OR-A5JO 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5JR                  TCGA-OR-A5K6 
"DEL PEAK  2(1Q43) WILD-TYPE" "DEL PEAK  2(1Q43) WILD-TYPE" 
                 TCGA-OR-A5K9 
"DEL PEAK  2(1Q43) WILD-TYPE" 
                             vv
clus                          T1+T2+T4
  DEL PEAK  2(1Q43) MUTATED          2
  DEL PEAK  2(1Q43) WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D14V5, binary
                             cls
clus                          0 1
  DEL PEAK  2(1Q43) MUTATED   1 2
  DEL PEAK  2(1Q43) WILD-TYPE 4 3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED      1    2
  DEL PEAK  2(1Q43) WILD-TYPE    4    3
        clus
vv       DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  FEMALE                         1                           4
  MALE                           2                           3

Clustering(15) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  6(4Q34.3) MUTATED   1 3
  DEL PEAK  6(4Q34.3) WILD-TYPE 5 1
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            4                             6 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            3                             1 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        37.15        11.31 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78        10.16        29.23       121.25        23.31 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        11.31                         10.16 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        37.15                        121.25 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       18.065                        38.005 
[1] "11.3 - 37.1 (18.1)"  "10.2 - 121.2 (38.0)"
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
[1] "hr="     "3.4e+09"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED         0        2        2
  DEL PEAK  6(4Q34.3) WILD-TYPE       3        0        2
D15V3, multiclass
          clus
vv         DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                            0                             3
  STAGE II                           2                             0
  STAGE IV                           2                             2
                               vv
clus                            T1+T2+T4
  DEL PEAK  6(4Q34.3) MUTATED          4
  DEL PEAK  6(4Q34.3) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D15V5, binary
                               cls
clus                            0 1
  DEL PEAK  6(4Q34.3) MUTATED   3 1
  DEL PEAK  6(4Q34.3) WILD-TYPE 2 4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      3    1
  DEL PEAK  6(4Q34.3) WILD-TYPE    2    4
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                           3                             2
  MALE                             1                             4

Clustering(16) Variable = DEL PEAK  7(4Q35.1) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  7(4Q35.1) MUTATED   0 3
  DEL PEAK  7(4Q35.1) WILD-TYPE 6 1
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                            3                             7 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                            3                             1 
$`DEL PEAK  7(4Q35.1) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JM 
       18.08        57.53        18.05 

$`DEL PEAK  7(4Q35.1) WILD-TYPE`
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 
       46.78        10.16        29.23       121.25        37.15        11.31 
TCGA-OU-A5PI 
       23.31 

  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                        18.05                         10.16 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                        57.53                        121.25 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                        18.08                         29.23 
[1] "18.1 - 57.5 (18.1)"  "10.2 - 121.2 (29.2)"
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
  "DEL PEAK  7(4Q35.1) MUTATED"   "DEL PEAK  7(4Q35.1) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK  7(4Q35.1) MUTATED" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
  "DEL PEAK  7(4Q35.1) MUTATED"   "DEL PEAK  7(4Q35.1) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK  7(4Q35.1) MUTATED" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
  "DEL PEAK  7(4Q35.1) MUTATED"   "DEL PEAK  7(4Q35.1) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK  7(4Q35.1) MUTATED" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
[1] "hr=" "5.2"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  DEL PEAK  7(4Q35.1) MUTATED         0        0        2
  DEL PEAK  7(4Q35.1) WILD-TYPE       3        2        2
D16V3, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  7(4Q35.1) MUTATED"
clus
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                            2                             7 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5JO                    TCGA-OR-A5JR 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OR-A5K6                    TCGA-OR-A5K9 
"DEL PEAK  7(4Q35.1) WILD-TYPE" "DEL PEAK  7(4Q35.1) WILD-TYPE" 
                   TCGA-OU-A5PI 
"DEL PEAK  7(4Q35.1) WILD-TYPE" 
                               vv
clus                            T1+T2+T4
  DEL PEAK  7(4Q35.1) MUTATED          2
  DEL PEAK  7(4Q35.1) WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D16V5, binary
                               cls
clus                            0 1
  DEL PEAK  7(4Q35.1) MUTATED   1 2
  DEL PEAK  7(4Q35.1) WILD-TYPE 4 3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED      1    2
  DEL PEAK  7(4Q35.1) WILD-TYPE    4    3
        clus
vv       DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  FEMALE                           1                             4
  MALE                             2                             3

Clustering(17) Variable = DEL PEAK 10(7Q32.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 10(7Q32.3) MUTATED   1 2
  DEL PEAK 10(7Q32.3) WILD-TYPE 5 2
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            3                             7 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            2                             2 
$`DEL PEAK 10(7Q32.3) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OR-A5K6 
       57.53        18.05        37.15 

$`DEL PEAK 10(7Q32.3) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K9 
       18.08        46.78        10.16        29.23       121.25        11.31 
TCGA-OU-A5PI 
       23.31 

  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                        18.05                         10.16 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                        57.53                        121.25 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                        37.15                         23.31 
[1] "18.1 - 57.5 (37.1)"  "10.2 - 121.2 (23.3)"
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"DEL PEAK 10(7Q32.3) WILD-TYPE"   "DEL PEAK 10(7Q32.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK 10(7Q32.3) MUTATED" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK 10(7Q32.3) WILD-TYPE"   "DEL PEAK 10(7Q32.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"DEL PEAK 10(7Q32.3) WILD-TYPE"   "DEL PEAK 10(7Q32.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK 10(7Q32.3) MUTATED" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK 10(7Q32.3) WILD-TYPE"   "DEL PEAK 10(7Q32.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"DEL PEAK 10(7Q32.3) WILD-TYPE"   "DEL PEAK 10(7Q32.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK 10(7Q32.3) MUTATED" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK 10(7Q32.3) WILD-TYPE"   "DEL PEAK 10(7Q32.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
[1] "hr=" "1.7"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  DEL PEAK 10(7Q32.3) MUTATED         0        1        1
  DEL PEAK 10(7Q32.3) WILD-TYPE       3        1        3
D17V3, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 10(7Q32.3) MUTATED"
clus
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            2                             7 
                   TCGA-OR-A5JB                    TCGA-OR-A5JI 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JJ                    TCGA-OR-A5JO 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K9 
"DEL PEAK 10(7Q32.3) WILD-TYPE" "DEL PEAK 10(7Q32.3) WILD-TYPE" 
                   TCGA-OU-A5PI 
"DEL PEAK 10(7Q32.3) WILD-TYPE" 
                               vv
clus                            T1+T2+T4
  DEL PEAK 10(7Q32.3) MUTATED          2
  DEL PEAK 10(7Q32.3) WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D17V5, binary
                               cls
clus                            0 1
  DEL PEAK 10(7Q32.3) MUTATED   2 1
  DEL PEAK 10(7Q32.3) WILD-TYPE 3 4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q32.3) MUTATED      2    1
  DEL PEAK 10(7Q32.3) WILD-TYPE    3    4
        clus
vv       DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE
  FEMALE                           2                             3
  MALE                             1                             4

Clustering(18) Variable = DEL PEAK 12(9P21.3) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 12(9P21.3) MUTATED   1 3
  DEL PEAK 12(9P21.3) WILD-TYPE 5 1
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                            4                             6 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                            3                             1 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OR-A5K9 
       57.53        18.05        37.15        11.31 

$`DEL PEAK 12(9P21.3) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OU-A5PI 
       18.08        46.78        10.16        29.23       121.25        23.31 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        11.31                         10.16 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        57.53                        121.25 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        27.60                         26.27 
[1] "11.3 - 57.5 (27.6)"  "10.2 - 121.2 (26.3)"
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JB                    TCGA-OR-A5JC 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-OR-A5JI                    TCGA-OR-A5JJ 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JM                    TCGA-OR-A5JO 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-OR-A5JR                    TCGA-OR-A5K6 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-OR-A5K9                    TCGA-OU-A5PI 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
[1] "hr=" "4.7"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IV
  DEL PEAK 12(9P21.3) MUTATED         0        2        1
  DEL PEAK 12(9P21.3) WILD-TYPE       3        0        3
D18V3, multiclass
          clus
vv         DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  STAGE I                            0                             3
  STAGE II                           2                             0
  STAGE IV                           1                             3
                               vv
clus                            T1+T2+T4
  DEL PEAK 12(9P21.3) MUTATED          3
  DEL PEAK 12(9P21.3) WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D18V5, binary
                               cls
clus                            0 1
  DEL PEAK 12(9P21.3) MUTATED   3 1
  DEL PEAK 12(9P21.3) WILD-TYPE 2 4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED      3    1
  DEL PEAK 12(9P21.3) WILD-TYPE    2    4
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  FEMALE                           3                             2
  MALE                             1                             4

Clustering(19) Variable = DEL PEAK 14(11P15.5) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 14(11P15.5) MUTATED   3 2
  DEL PEAK 14(11P15.5) WILD-TYPE 3 2
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                             5                              5 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                             2                              2 
$`DEL PEAK 14(11P15.5) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
       57.53        46.78        37.15        11.31        23.31 

$`DEL PEAK 14(11P15.5) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR 
       18.08        10.16        18.05        29.23       121.25 

  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                         11.31                          10.16 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                         57.53                         121.25 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                         37.15                          18.08 
[1] "11.3 - 57.5 (37.1)"  "10.2 - 121.2 (18.1)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 14(11P15.5) WILD-TYPE"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 14(11P15.5) MUTATED" "DEL PEAK 14(11P15.5) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 14(11P15.5) WILD-TYPE" "DEL PEAK 14(11P15.5) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 14(11P15.5) WILD-TYPE"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 14(11P15.5) MUTATED"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 14(11P15.5) WILD-TYPE"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 14(11P15.5) MUTATED" "DEL PEAK 14(11P15.5) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 14(11P15.5) WILD-TYPE" "DEL PEAK 14(11P15.5) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 14(11P15.5) WILD-TYPE"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 14(11P15.5) MUTATED"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 14(11P15.5) WILD-TYPE"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 14(11P15.5) MUTATED" "DEL PEAK 14(11P15.5) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 14(11P15.5) WILD-TYPE" "DEL PEAK 14(11P15.5) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 14(11P15.5) WILD-TYPE"   "DEL PEAK 14(11P15.5) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 14(11P15.5) MUTATED"   "DEL PEAK 14(11P15.5) MUTATED" 
[1] "hr=" "1.1"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 14(11P15.5) MUTATED         1        2        1
  DEL PEAK 14(11P15.5) WILD-TYPE       2        0        3
D19V3, multiclass
          clus
vv         DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  STAGE I                             1                              2
  STAGE II                            2                              0
  STAGE IV                            1                              3
                                vv
clus                             T1+T2+T4
  DEL PEAK 14(11P15.5) MUTATED          4
  DEL PEAK 14(11P15.5) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D19V5, binary
                                cls
clus                             0 1
  DEL PEAK 14(11P15.5) MUTATED   3 2
  DEL PEAK 14(11P15.5) WILD-TYPE 2 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED      3    2
  DEL PEAK 14(11P15.5) WILD-TYPE    2    3
        clus
vv       DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  FEMALE                            3                              2
  MALE                              2                              3

Clustering(20) Variable = DEL PEAK 15(11Q14.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 15(11Q14.1) MUTATED   3 2
  DEL PEAK 15(11Q14.1) WILD-TYPE 3 2
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                             5                              5 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                             2                              2 
$`DEL PEAK 15(11Q14.1) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
       57.53        46.78        37.15        11.31        23.31 

$`DEL PEAK 15(11Q14.1) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR 
       18.08        10.16        18.05        29.23       121.25 

  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                         11.31                          10.16 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                         57.53                         121.25 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                         37.15                          18.08 
[1] "11.3 - 57.5 (37.1)"  "10.2 - 121.2 (18.1)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 15(11Q14.1) WILD-TYPE"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 15(11Q14.1) MUTATED" "DEL PEAK 15(11Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 15(11Q14.1) WILD-TYPE" "DEL PEAK 15(11Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 15(11Q14.1) WILD-TYPE"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 15(11Q14.1) MUTATED"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 15(11Q14.1) WILD-TYPE"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 15(11Q14.1) MUTATED" "DEL PEAK 15(11Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 15(11Q14.1) WILD-TYPE" "DEL PEAK 15(11Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 15(11Q14.1) WILD-TYPE"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 15(11Q14.1) MUTATED"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 15(11Q14.1) WILD-TYPE"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 15(11Q14.1) MUTATED" "DEL PEAK 15(11Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 15(11Q14.1) WILD-TYPE" "DEL PEAK 15(11Q14.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 15(11Q14.1) WILD-TYPE"   "DEL PEAK 15(11Q14.1) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 15(11Q14.1) MUTATED"   "DEL PEAK 15(11Q14.1) MUTATED" 
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 15(11Q14.1) MUTATED         1        2        1
  DEL PEAK 15(11Q14.1) WILD-TYPE       2        0        3
D20V3, multiclass
          clus
vv         DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  STAGE I                             1                              2
  STAGE II                            2                              0
  STAGE IV                            1                              3
                                vv
clus                             T1+T2+T4
  DEL PEAK 15(11Q14.1) MUTATED          4
  DEL PEAK 15(11Q14.1) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D20V5, binary
                                cls
clus                             0 1
  DEL PEAK 15(11Q14.1) MUTATED   3 2
  DEL PEAK 15(11Q14.1) WILD-TYPE 2 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED      3    2
  DEL PEAK 15(11Q14.1) WILD-TYPE    2    3
        clus
vv       DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  FEMALE                            3                              2
  MALE                              2                              3

Clustering(21) Variable = DEL PEAK 17(13Q14.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 17(13Q14.2) MUTATED   2 3
  DEL PEAK 17(13Q14.2) WILD-TYPE 4 1
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                             5                              5 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                             3                              1 
$`DEL PEAK 17(13Q14.2) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5K9 TCGA-OU-A5PI 
       18.08        57.53        46.78        11.31        23.31 

$`DEL PEAK 17(13Q14.2) WILD-TYPE`
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       10.16        18.05        29.23       121.25        37.15 

  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                         11.31                          10.16 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                         57.53                         121.25 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                         23.31                          29.23 
[1] "11.3 - 57.5 (23.3)"  "10.2 - 121.2 (29.2)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 17(13Q14.2) MUTATED"   "DEL PEAK 17(13Q14.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 17(13Q14.2) MUTATED" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 17(13Q14.2) MUTATED"   "DEL PEAK 17(13Q14.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 17(13Q14.2) MUTATED"   "DEL PEAK 17(13Q14.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 17(13Q14.2) MUTATED" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 17(13Q14.2) MUTATED"   "DEL PEAK 17(13Q14.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 17(13Q14.2) MUTATED"   "DEL PEAK 17(13Q14.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 17(13Q14.2) MUTATED" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 17(13Q14.2) MUTATED"   "DEL PEAK 17(13Q14.2) MUTATED" 
[1] "hr=" "2.7"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 17(13Q14.2) MUTATED         1        1        2
  DEL PEAK 17(13Q14.2) WILD-TYPE       2        1        2
D21V3, multiclass
          clus
vv         DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  STAGE I                             1                              2
  STAGE II                            1                              1
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  DEL PEAK 17(13Q14.2) MUTATED          4
  DEL PEAK 17(13Q14.2) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D21V5, binary
                                cls
clus                             0 1
  DEL PEAK 17(13Q14.2) MUTATED   2 3
  DEL PEAK 17(13Q14.2) WILD-TYPE 3 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED      2    3
  DEL PEAK 17(13Q14.2) WILD-TYPE    3    2
        clus
vv       DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  FEMALE                            2                              3
  MALE                              3                              2

Clustering(22) Variable = DEL PEAK 21(17Q11.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 21(17Q11.2) MUTATED   1 3
  DEL PEAK 21(17Q11.2) WILD-TYPE 5 1
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                             4                              6 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                             3                              1 
$`DEL PEAK 21(17Q11.2) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5K9 TCGA-OU-A5PI 
       18.08        57.53        11.31        23.31 

$`DEL PEAK 21(17Q11.2) WILD-TYPE`
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       46.78        10.16        18.05        29.23       121.25        37.15 

  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                         11.31                          10.16 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                         57.53                         121.25 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                        20.695                         33.190 
[1] "11.3 - 57.5 (20.7)"  "10.2 - 121.2 (33.2)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 21(17Q11.2) MUTATED"   "DEL PEAK 21(17Q11.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 21(17Q11.2) MUTATED"   "DEL PEAK 21(17Q11.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 21(17Q11.2) MUTATED"   "DEL PEAK 21(17Q11.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 21(17Q11.2) MUTATED"   "DEL PEAK 21(17Q11.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 21(17Q11.2) MUTATED"   "DEL PEAK 21(17Q11.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 21(17Q11.2) WILD-TYPE" "DEL PEAK 21(17Q11.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 21(17Q11.2) MUTATED"   "DEL PEAK 21(17Q11.2) MUTATED" 
[1] "hr=" "3.9"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 21(17Q11.2) MUTATED         0        1        2
  DEL PEAK 21(17Q11.2) WILD-TYPE       3        1        2
D22V3, multiclass
          clus
vv         DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE
  STAGE I                             0                              3
  STAGE II                            1                              1
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  DEL PEAK 21(17Q11.2) MUTATED          3
  DEL PEAK 21(17Q11.2) WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D22V5, binary
                                cls
clus                             0 1
  DEL PEAK 21(17Q11.2) MUTATED   2 2
  DEL PEAK 21(17Q11.2) WILD-TYPE 3 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(17Q11.2) MUTATED      2    2
  DEL PEAK 21(17Q11.2) WILD-TYPE    3    3
        clus
vv       DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE
  FEMALE                            2                              3
  MALE                              2                              3

Clustering(23) Variable = DEL PEAK 22(17Q21.31) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 22(17Q21.31) MUTATED   1 2
  DEL PEAK 22(17Q21.31) WILD-TYPE 5 2
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                              3                               7 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                              2                               2 
$`DEL PEAK 22(17Q21.31) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5K9 TCGA-OU-A5PI 
       57.53        11.31        23.31 

$`DEL PEAK 22(17Q21.31) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR 
       18.08        46.78        10.16        18.05        29.23       121.25 
TCGA-OR-A5K6 
       37.15 

  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                          11.31                           10.16 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                          57.53                          121.25 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                          23.31                           29.23 
[1] "11.3 - 57.5 (23.3)"  "10.2 - 121.2 (29.2)"
                     TCGA-OR-A5JB                      TCGA-OR-A5JC 
"DEL PEAK 22(17Q21.31) WILD-TYPE"   "DEL PEAK 22(17Q21.31) MUTATED" 
                     TCGA-OR-A5JI                      TCGA-OR-A5JJ 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JM                      TCGA-OR-A5JO 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JR                      TCGA-OR-A5K6 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5K9                      TCGA-OU-A5PI 
  "DEL PEAK 22(17Q21.31) MUTATED"   "DEL PEAK 22(17Q21.31) MUTATED" 
                     TCGA-OR-A5JB                      TCGA-OR-A5JC 
"DEL PEAK 22(17Q21.31) WILD-TYPE"   "DEL PEAK 22(17Q21.31) MUTATED" 
                     TCGA-OR-A5JI                      TCGA-OR-A5JJ 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JM                      TCGA-OR-A5JO 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JR                      TCGA-OR-A5K6 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5K9                      TCGA-OU-A5PI 
  "DEL PEAK 22(17Q21.31) MUTATED"   "DEL PEAK 22(17Q21.31) MUTATED" 
                     TCGA-OR-A5JB                      TCGA-OR-A5JC 
"DEL PEAK 22(17Q21.31) WILD-TYPE"   "DEL PEAK 22(17Q21.31) MUTATED" 
                     TCGA-OR-A5JI                      TCGA-OR-A5JJ 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JM                      TCGA-OR-A5JO 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JR                      TCGA-OR-A5K6 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5K9                      TCGA-OU-A5PI 
  "DEL PEAK 22(17Q21.31) MUTATED"   "DEL PEAK 22(17Q21.31) MUTATED" 
[1] "hr=" "2"  
D23V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IV
  DEL PEAK 22(17Q21.31) MUTATED         0        1        1
  DEL PEAK 22(17Q21.31) WILD-TYPE       3        1        3
D23V3, multiclass
[1] "Remove cluster labels:"        "DEL PEAK 22(17Q21.31) MUTATED"
clus
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                              2                               7 
                     TCGA-OR-A5JB                      TCGA-OR-A5JI 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JJ                      TCGA-OR-A5JM 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5JO                      TCGA-OR-A5JR 
"DEL PEAK 22(17Q21.31) WILD-TYPE" "DEL PEAK 22(17Q21.31) WILD-TYPE" 
                     TCGA-OR-A5K6 
"DEL PEAK 22(17Q21.31) WILD-TYPE" 
                                 vv
clus                              T1+T2+T4
  DEL PEAK 22(17Q21.31) MUTATED          2
  DEL PEAK 22(17Q21.31) WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D23V5, binary
                                 cls
clus                              0 1
  DEL PEAK 22(17Q21.31) MUTATED   2 1
  DEL PEAK 22(17Q21.31) WILD-TYPE 3 4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(17Q21.31) MUTATED      2    1
  DEL PEAK 22(17Q21.31) WILD-TYPE    3    4
        clus
vv       DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE
  FEMALE                             2                               3
  MALE                               1                               4

Clustering(24) Variable = DEL PEAK 23(17Q24.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 23(17Q24.2) MUTATED   2 3
  DEL PEAK 23(17Q24.2) WILD-TYPE 4 1
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                             5                              5 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                             3                              1 
$`DEL PEAK 23(17Q24.2) MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
       57.53        18.05        37.15        11.31        23.31 

$`DEL PEAK 23(17Q24.2) WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR 
       18.08        46.78        10.16        29.23       121.25 

  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                         11.31                          10.16 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                         57.53                         121.25 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                         23.31                          29.23 
[1] "11.3 - 57.5 (23.3)"  "10.2 - 121.2 (29.2)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 23(17Q24.2) WILD-TYPE"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 23(17Q24.2) WILD-TYPE" "DEL PEAK 23(17Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 23(17Q24.2) MUTATED" "DEL PEAK 23(17Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 23(17Q24.2) WILD-TYPE"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 23(17Q24.2) MUTATED"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 23(17Q24.2) WILD-TYPE"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 23(17Q24.2) WILD-TYPE" "DEL PEAK 23(17Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 23(17Q24.2) MUTATED" "DEL PEAK 23(17Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 23(17Q24.2) WILD-TYPE"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 23(17Q24.2) MUTATED"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
"DEL PEAK 23(17Q24.2) WILD-TYPE"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 23(17Q24.2) WILD-TYPE" "DEL PEAK 23(17Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 23(17Q24.2) MUTATED" "DEL PEAK 23(17Q24.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 23(17Q24.2) WILD-TYPE"   "DEL PEAK 23(17Q24.2) MUTATED" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 23(17Q24.2) MUTATED"   "DEL PEAK 23(17Q24.2) MUTATED" 
[1] "hr=" "3.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 23(17Q24.2) MUTATED         0        2        2
  DEL PEAK 23(17Q24.2) WILD-TYPE       3        0        2
D24V3, multiclass
          clus
vv         DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE
  STAGE I                             0                              3
  STAGE II                            2                              0
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  DEL PEAK 23(17Q24.2) MUTATED          4
  DEL PEAK 23(17Q24.2) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D24V5, binary
                                cls
clus                             0 1
  DEL PEAK 23(17Q24.2) MUTATED   4 1
  DEL PEAK 23(17Q24.2) WILD-TYPE 1 4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.2) MUTATED      4    1
  DEL PEAK 23(17Q24.2) WILD-TYPE    1    4
        clus
vv       DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE
  FEMALE                            4                              1
  MALE                              1                              4

Clustering(25) Variable = DEL PEAK 24(18Q21.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 24(18Q21.2) MUTATED   2 3
  DEL PEAK 24(18Q21.2) WILD-TYPE 4 1
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                             5                              5 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                             3                              1 
$`DEL PEAK 24(18Q21.2) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OU-A5PI 
       18.08        57.53        46.78        18.05        23.31 

$`DEL PEAK 24(18Q21.2) WILD-TYPE`
TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 
       10.16        29.23       121.25        37.15        11.31 

  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                         18.05                          10.16 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                         57.53                         121.25 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                         23.31                          29.23 
[1] "18.1 - 57.5 (23.3)"  "10.2 - 121.2 (29.2)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 24(18Q21.2) MUTATED"   "DEL PEAK 24(18Q21.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 24(18Q21.2) MUTATED" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 24(18Q21.2) MUTATED" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 24(18Q21.2) WILD-TYPE" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"DEL PEAK 24(18Q21.2) WILD-TYPE"   "DEL PEAK 24(18Q21.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 24(18Q21.2) MUTATED"   "DEL PEAK 24(18Q21.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 24(18Q21.2) MUTATED" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 24(18Q21.2) MUTATED" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 24(18Q21.2) WILD-TYPE" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"DEL PEAK 24(18Q21.2) WILD-TYPE"   "DEL PEAK 24(18Q21.2) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 24(18Q21.2) MUTATED"   "DEL PEAK 24(18Q21.2) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 24(18Q21.2) MUTATED" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 24(18Q21.2) MUTATED" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 24(18Q21.2) WILD-TYPE" "DEL PEAK 24(18Q21.2) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
"DEL PEAK 24(18Q21.2) WILD-TYPE"   "DEL PEAK 24(18Q21.2) MUTATED" 
[1] "hr=" "2.3"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 24(18Q21.2) MUTATED         1        0        3
  DEL PEAK 24(18Q21.2) WILD-TYPE       2        2        1
D25V3, multiclass
          clus
vv         DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE
  STAGE I                             1                              2
  STAGE II                            0                              2
  STAGE IV                            3                              1
                                vv
clus                             T1+T2+T4
  DEL PEAK 24(18Q21.2) MUTATED          4
  DEL PEAK 24(18Q21.2) WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D25V5, binary
                                cls
clus                             0 1
  DEL PEAK 24(18Q21.2) MUTATED   2 3
  DEL PEAK 24(18Q21.2) WILD-TYPE 3 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(18Q21.2) MUTATED      2    3
  DEL PEAK 24(18Q21.2) WILD-TYPE    3    2
        clus
vv       DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE
  FEMALE                            2                              3
  MALE                              3                              2

Clustering(26) Variable = DEL PEAK 25(20P12.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 25(20P12.1) MUTATED   0 3
  DEL PEAK 25(20P12.1) WILD-TYPE 6 1
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             3                              7 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             3                              1 
$`DEL PEAK 25(20P12.1) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5K9 
       18.08        18.05        11.31 

$`DEL PEAK 25(20P12.1) WILD-TYPE`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       57.53        46.78        10.16        29.23       121.25        37.15 
TCGA-OU-A5PI 
       23.31 

  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         11.31                          10.16 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         18.08                         121.25 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         18.05                          37.15 
[1] "11.3 - 18.1 (18.1)"  "10.2 - 121.2 (37.1)"
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 25(20P12.1) WILD-TYPE" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 25(20P12.1) WILD-TYPE" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 25(20P12.1) WILD-TYPE" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 25(20P12.1) WILD-TYPE" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
"DEL PEAK 25(20P12.1) WILD-TYPE" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
"DEL PEAK 25(20P12.1) WILD-TYPE" "DEL PEAK 25(20P12.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 25(20P12.1) MUTATED" "DEL PEAK 25(20P12.1) WILD-TYPE" 
[1] "hr="     "1.4e+10"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 25(20P12.1) MUTATED         0        1        2
  DEL PEAK 25(20P12.1) WILD-TYPE       3        1        2
D26V3, multiclass
          clus
vv         DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  STAGE I                             0                              3
  STAGE II                            1                              1
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  DEL PEAK 25(20P12.1) MUTATED          3
  DEL PEAK 25(20P12.1) WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D26V5, binary
                                cls
clus                             0 1
  DEL PEAK 25(20P12.1) MUTATED   2 1
  DEL PEAK 25(20P12.1) WILD-TYPE 3 4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED      2    1
  DEL PEAK 25(20P12.1) WILD-TYPE    3    4
        clus
vv       DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  FEMALE                            2                              3
  MALE                              1                              4

Clustering(27) Variable = DEL PEAK 26(22Q12.1) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 26(22Q12.1) MUTATED   3 3
  DEL PEAK 26(22Q12.1) WILD-TYPE 3 1
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                             6                              4 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                             3                              1 
$`DEL PEAK 26(22Q12.1) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JR TCGA-OR-A5K9 TCGA-OU-A5PI 
       18.08        57.53        46.78       121.25        11.31        23.31 

$`DEL PEAK 26(22Q12.1) WILD-TYPE`
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 
       10.16        18.05        29.23        37.15 

  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                         11.31                          10.16 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                        121.25                          37.15 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                        35.045                         23.640 
[1] "11.3 - 121.2 (35.0)" "10.2 - 37.1 (23.6)" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 26(22Q12.1) MUTATED"   "DEL PEAK 26(22Q12.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 26(22Q12.1) MUTATED" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 26(22Q12.1) WILD-TYPE" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "DEL PEAK 26(22Q12.1) MUTATED" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 26(22Q12.1) MUTATED"   "DEL PEAK 26(22Q12.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 26(22Q12.1) MUTATED"   "DEL PEAK 26(22Q12.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 26(22Q12.1) MUTATED" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 26(22Q12.1) WILD-TYPE" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "DEL PEAK 26(22Q12.1) MUTATED" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 26(22Q12.1) MUTATED"   "DEL PEAK 26(22Q12.1) MUTATED" 
                    TCGA-OR-A5JB                     TCGA-OR-A5JC 
  "DEL PEAK 26(22Q12.1) MUTATED"   "DEL PEAK 26(22Q12.1) MUTATED" 
                    TCGA-OR-A5JI                     TCGA-OR-A5JJ 
  "DEL PEAK 26(22Q12.1) MUTATED" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5JM                     TCGA-OR-A5JO 
"DEL PEAK 26(22Q12.1) WILD-TYPE" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5JR                     TCGA-OR-A5K6 
  "DEL PEAK 26(22Q12.1) MUTATED" "DEL PEAK 26(22Q12.1) WILD-TYPE" 
                    TCGA-OR-A5K9                     TCGA-OU-A5PI 
  "DEL PEAK 26(22Q12.1) MUTATED"   "DEL PEAK 26(22Q12.1) MUTATED" 
[1] "hr=" "1"  
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IV
  DEL PEAK 26(22Q12.1) MUTATED         2        1        2
  DEL PEAK 26(22Q12.1) WILD-TYPE       1        1        2
D27V3, multiclass
          clus
vv         DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  STAGE I                             2                              1
  STAGE II                            1                              1
  STAGE IV                            2                              2
                                vv
clus                             T1+T2+T4
  DEL PEAK 26(22Q12.1) MUTATED          5
  DEL PEAK 26(22Q12.1) WILD-TYPE        4
[1] "NOT AVAILABLE: table dimension [2x1]"
D27V5, binary
                                cls
clus                             0 1
  DEL PEAK 26(22Q12.1) MUTATED   2 4
  DEL PEAK 26(22Q12.1) WILD-TYPE 3 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED      2    4
  DEL PEAK 26(22Q12.1) WILD-TYPE    3    1
        clus
vv       DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  FEMALE                            2                              3
  MALE                              4                              1
> q(save="no")
