
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/6156368/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/6156368/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 80 to 34."
[1] 34 10
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                 5 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                 5 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                 5 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                 5 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                 5 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                 5 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                 6 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                 6 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 7 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 7 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 7 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 7 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                 6 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                 6 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 5 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 5 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                  7 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                  7 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                  4 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                  4 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                  5 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                  5 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                  5 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                  5 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                  5 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                  5 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                  3 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                  3 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                  4 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                  4 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  7 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  7 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                  5 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                  5 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                  5 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                  5 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                 5 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                 5 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                 6 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                 6 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                 7 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                 7 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                 7 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                 7 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                 7 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                 7 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                 7 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                 7 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  5 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  5 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  5 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  5 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                  5 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                  5 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                  6 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                  6 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                  5 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                  5 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                  7 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                  7 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  6 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  6 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                  6 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                  6 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 6                  4 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 6                  4 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                 7 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                 7 
[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 = 4P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2               0 1
  4P GAIN MUTATED   4 1
  4P GAIN WILD-TYPE 2 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                 5 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 3 
$`4P GAIN 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 

$`4P GAIN 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 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            10.16             11.31 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           121.25             37.15 
  4P GAIN MUTATED 4P GAIN 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        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
[1] "hr="     "1.7e+09"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  4P GAIN MUTATED         2        0        2
  4P GAIN WILD-TYPE       1        2        2
D1V3, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                2                 1
  STAGE II               0                 2
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  4P GAIN MUTATED          4
  4P GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D1V5, binary
                   cls
clus                0 1
  4P GAIN MUTATED   1 4
  4P GAIN WILD-TYPE 4 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    4
  4P GAIN WILD-TYPE    4    1
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                 4
  MALE                 4                 1

Clustering(2) Variable = 4Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2               0 1
  4Q GAIN MUTATED   4 1
  4Q GAIN WILD-TYPE 2 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                 5 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                 3 
$`4Q GAIN 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 

$`4Q GAIN 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 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            10.16             11.31 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           121.25             37.15 
  4Q GAIN MUTATED 4Q GAIN 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        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
[1] "hr="     "1.7e+09"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  4Q GAIN MUTATED         2        0        2
  4Q GAIN WILD-TYPE       1        2        2
D2V3, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                2                 1
  STAGE II               0                 2
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  4Q GAIN MUTATED          4
  4Q GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D2V5, binary
                   cls
clus                0 1
  4Q GAIN MUTATED   1 4
  4Q GAIN WILD-TYPE 4 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    4
  4Q GAIN WILD-TYPE    4    1
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                 4
  MALE                 4                 1

Clustering(3) Variable = 5P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2               0 1
  5P GAIN MUTATED   4 1
  5P GAIN WILD-TYPE 2 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                 5 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 3 
$`5P GAIN 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 

$`5P GAIN 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 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            10.16             11.31 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           121.25             37.15 
  5P GAIN MUTATED 5P GAIN 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        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
[1] "hr="     "1.7e+09"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  5P GAIN MUTATED         2        0        2
  5P GAIN WILD-TYPE       1        2        2
D3V3, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                2                 1
  STAGE II               0                 2
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  5P GAIN MUTATED          4
  5P GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D3V5, binary
                   cls
clus                0 1
  5P GAIN MUTATED   1 4
  5P GAIN WILD-TYPE 4 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1    4
  5P GAIN WILD-TYPE    4    1
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               1                 4
  MALE                 4                 1

Clustering(4) Variable = 5Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2               0 1
  5Q GAIN MUTATED   3 1
  5Q GAIN WILD-TYPE 3 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                 6 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                 3 
$`5Q GAIN MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OU-A5PI 
       57.53        46.78        10.16        23.31 

$`5Q GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        29.23       121.25        37.15        11.31 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            10.16             11.31 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            57.53            121.25 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           35.045            23.655 
[1] "10.2 - 57.5 (35.0)"  "11.3 - 121.2 (23.7)"
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
[1] "hr=" "2.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  5Q GAIN MUTATED         1        0        2
  5Q GAIN WILD-TYPE       2        2        2
D4V3, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                1                 2
  STAGE II               0                 2
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  5Q GAIN MUTATED          3
  5Q GAIN WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D4V5, binary
                   cls
clus                0 1
  5Q GAIN MUTATED   1 3
  5Q GAIN WILD-TYPE 4 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    3
  5Q GAIN WILD-TYPE    4    2
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               1                 4
  MALE                 3                 2

Clustering(5) Variable = 7P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2               0 1
  7P GAIN MUTATED   3 0
  7P GAIN WILD-TYPE 3 4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 7 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 4 
$`7P GAIN MUTATED`
TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OU-A5PI 
       10.16       121.25        23.31 

$`7P GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        57.53        46.78        18.05        29.23        37.15 
TCGA-OR-A5K9 
       11.31 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            10.16             11.31 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           121.25             57.53 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            23.31             29.23 
[1] "10.2 - 121.2 (23.3)" "11.3 - 57.5 (29.2)" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
[1] "hr="   "1e+09"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  7P GAIN MUTATED         1        0        2
  7P GAIN WILD-TYPE       2        2        2
D5V3, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                1                 2
  STAGE II               0                 2
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  7P GAIN MUTATED          3
  7P GAIN WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D5V5, binary
                   cls
clus                0 1
  7P GAIN MUTATED   1 2
  7P GAIN WILD-TYPE 4 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1    2
  7P GAIN WILD-TYPE    4    3
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               1                 4
  MALE                 2                 3

Clustering(6) Variable = 7Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2               0 1
  7Q GAIN MUTATED   3 0
  7Q GAIN WILD-TYPE 3 4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 7 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 4 
$`7Q GAIN MUTATED`
TCGA-OR-A5JJ TCGA-OR-A5JR TCGA-OU-A5PI 
       10.16       121.25        23.31 

$`7Q GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        57.53        46.78        18.05        29.23        37.15 
TCGA-OR-A5K9 
       11.31 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            10.16             11.31 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           121.25             57.53 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            23.31             29.23 
[1] "10.2 - 121.2 (23.3)" "11.3 - 57.5 (29.2)" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
[1] "hr="   "1e+09"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  7Q GAIN MUTATED         1        0        2
  7Q GAIN WILD-TYPE       2        2        2
D6V3, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                1                 2
  STAGE II               0                 2
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  7Q GAIN MUTATED          3
  7Q GAIN WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D6V5, binary
                   cls
clus                0 1
  7Q GAIN MUTATED   1 2
  7Q GAIN WILD-TYPE 4 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1    2
  7Q GAIN WILD-TYPE    4    3
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               1                 4
  MALE                 2                 3

Clustering(7) Variable = 8P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2               0 1
  8P GAIN MUTATED   1 3
  8P GAIN WILD-TYPE 5 1
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                 6 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                 1 
$`8P GAIN MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OR-A5JR TCGA-OR-A5K9 
       57.53        18.05       121.25        11.31 

$`8P GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OU-A5PI 
       18.08        46.78        10.16        29.23        37.15        23.31 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            11.31             10.16 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           121.25             46.78 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            37.79             26.27 
[1] "11.3 - 121.2 (37.8)" "10.2 - 46.8 (26.3)" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
[1] "hr=" "3.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  8P GAIN MUTATED         1        1        1
  8P GAIN WILD-TYPE       2        1        3
D7V3, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                1                 2
  STAGE II               1                 1
  STAGE IV               1                 3
                   vv
clus                T1+T2+T4
  8P GAIN MUTATED          3
  8P GAIN WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D7V5, binary
                   cls
clus                0 1
  8P GAIN MUTATED   2 2
  8P GAIN WILD-TYPE 3 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    2
  8P GAIN WILD-TYPE    3    3
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               2                 3
  MALE                 2                 3

Clustering(8) Variable = 8Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2               0 1
  8Q GAIN MUTATED   2 3
  8Q GAIN WILD-TYPE 4 1
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 5 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                3                 1 
$`8Q GAIN MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JR TCGA-OR-A5K9 
       57.53        10.16        18.05       121.25        11.31 

$`8Q GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OU-A5PI 
       18.08        46.78        29.23        37.15        23.31 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            10.16             18.08 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           121.25             46.78 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.05             29.23 
[1] "10.2 - 121.2 (18.1)" "18.1 - 46.8 (29.2)" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
[1] "hr=" "3.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  8Q GAIN MUTATED         1        1        2
  8Q GAIN WILD-TYPE       2        1        2
D8V3, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                1                 2
  STAGE II               1                 1
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  8Q GAIN MUTATED          4
  8Q GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D8V5, binary
                   cls
clus                0 1
  8Q GAIN MUTATED   2 3
  8Q GAIN WILD-TYPE 3 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    3
  8Q GAIN WILD-TYPE    3    2
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               2                 3
  MALE                 3                 2

Clustering(9) Variable = 10Q GAIN MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                0 1
  10Q GAIN MUTATED   1 2
  10Q GAIN WILD-TYPE 5 2
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                  7 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                  2 
$`10Q GAIN MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OU-A5PI 
       57.53        18.05        23.31 

$`10Q GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       18.08        46.78        10.16        29.23       121.25        37.15 
TCGA-OR-A5K9 
       11.31 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             18.05              10.16 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             57.53             121.25 
  10Q GAIN MUTATED 10Q GAIN 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         TCGA-OR-A5JI 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "10Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "10Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "10Q GAIN MUTATED" 
[1] "hr=" "1.7"
D9V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  10Q GAIN MUTATED         0        0        2
  10Q GAIN WILD-TYPE       3        2        2
D9V3, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                  7 
        TCGA-OR-A5JB         TCGA-OR-A5JI         TCGA-OR-A5JJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5JO         TCGA-OR-A5JR         TCGA-OR-A5K6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-OR-A5K9 
"10Q GAIN WILD-TYPE" 
                    vv
clus                 T1+T2+T4
  10Q GAIN MUTATED          2
  10Q GAIN WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D9V5, binary
                    cls
clus                 0 1
  10Q GAIN MUTATED   2 1
  10Q GAIN WILD-TYPE 3 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE    3    4
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                  3
  MALE                  1                  4

Clustering(10) Variable = 12P GAIN MUTATION ANALYSIS
D10V1, survival
                    sevent
clus2                0 1
  12P GAIN MUTATED   4 2
  12P GAIN WILD-TYPE 2 2
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                  4 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  2 
$`12P GAIN MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JR TCGA-OU-A5PI 
       57.53        46.78        10.16        18.05       121.25        23.31 

$`12P GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        29.23        37.15        11.31 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             10.16              11.31 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            121.25              37.15 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            35.045             23.655 
[1] "10.2 - 121.2 (35.0)" "11.3 - 37.1 (23.7)" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "12P GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "12P GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "12P GAIN MUTATED" 
[1] "hr=" "2.8"
D10V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  12P GAIN MUTATED         2        0        3
  12P GAIN WILD-TYPE       1        2        1
D10V3, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 2                  1
  STAGE II                0                  2
  STAGE IV                3                  1
                    vv
clus                 T1+T2+T4
  12P GAIN MUTATED          5
  12P GAIN WILD-TYPE        4
[1] "NOT AVAILABLE: table dimension [2x1]"
D10V5, binary
                    cls
clus                 0 1
  12P GAIN MUTATED   2 4
  12P GAIN WILD-TYPE 3 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    4
  12P GAIN WILD-TYPE    3    1
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                  3
  MALE                  4                  1

Clustering(11) Variable = 12Q GAIN MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                0 1
  12Q GAIN MUTATED   4 1
  12Q GAIN WILD-TYPE 2 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                  5 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  3 
$`12Q GAIN 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 

$`12Q GAIN 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 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             10.16              11.31 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            121.25              37.15 
  12Q GAIN MUTATED 12Q GAIN 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         TCGA-OR-A5JI 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "12Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "12Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "12Q GAIN MUTATED" 
[1] "hr="     "1.7e+09"
D11V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  12Q GAIN MUTATED         2        0        2
  12Q GAIN WILD-TYPE       1        2        2
D11V3, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 2                  1
  STAGE II                0                  2
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  12Q GAIN MUTATED          4
  12Q GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D11V5, binary
                    cls
clus                 0 1
  12Q GAIN MUTATED   1 4
  12Q GAIN WILD-TYPE 4 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    4
  12Q GAIN WILD-TYPE    4    1
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                  4
  MALE                  4                  1

Clustering(12) Variable = 16P GAIN MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                0 1
  16P GAIN MUTATED   4 1
  16P GAIN WILD-TYPE 2 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                  5 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  3 
$`16P GAIN 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 

$`16P GAIN 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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             10.16              11.31 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            121.25              37.15 
  16P GAIN MUTATED 16P GAIN 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         TCGA-OR-A5JI 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "16P GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "16P GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "16P GAIN MUTATED" 
[1] "hr="     "1.7e+09"
D12V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  16P GAIN MUTATED         2        0        2
  16P GAIN WILD-TYPE       1        2        2
D12V3, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 2                  1
  STAGE II                0                  2
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  16P GAIN MUTATED          4
  16P GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D12V5, binary
                    cls
clus                 0 1
  16P GAIN MUTATED   1 4
  16P GAIN WILD-TYPE 4 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    4
  16P GAIN WILD-TYPE    4    1
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                1                  4
  MALE                  4                  1

Clustering(13) Variable = 16Q GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                0 1
  16Q GAIN MUTATED   4 1
  16Q GAIN WILD-TYPE 2 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                  5 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  3 
$`16Q GAIN 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 

$`16Q GAIN 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 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             10.16              11.31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            121.25              37.15 
  16Q GAIN MUTATED 16Q GAIN 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         TCGA-OR-A5JI 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "16Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "16Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "16Q GAIN MUTATED" 
[1] "hr="     "1.7e+09"
D13V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  16Q GAIN MUTATED         2        0        2
  16Q GAIN WILD-TYPE       1        2        2
D13V3, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 2                  1
  STAGE II                0                  2
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  16Q GAIN MUTATED          4
  16Q GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D13V5, binary
                    cls
clus                 0 1
  16Q GAIN MUTATED   1 4
  16Q GAIN WILD-TYPE 4 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    4
  16Q GAIN WILD-TYPE    4    1
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                1                  4
  MALE                  4                  1

Clustering(14) Variable = 19P GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                0 1
  19P GAIN MUTATED   4 3
  19P GAIN WILD-TYPE 2 1
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                  3 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                  1 
$`19P GAIN 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 

$`19P GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        29.23        37.15 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             10.16              18.08 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            121.25              37.15 
  19P GAIN MUTATED 19P GAIN 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         TCGA-OR-A5JI 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-OU-A5PI 
  "19P GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-OU-A5PI 
  "19P GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-OU-A5PI 
  "19P GAIN MUTATED" 
[1] "hr=" "1.2"
D14V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  19P GAIN MUTATED         2        1        3
  19P GAIN WILD-TYPE       1        1        1
D14V3, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                 2                  1
  STAGE II                1                  1
  STAGE IV                3                  1
                    vv
clus                 T1+T2+T4
  19P GAIN MUTATED          6
  19P GAIN WILD-TYPE        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D14V5, binary
                    cls
clus                 0 1
  19P GAIN MUTATED   3 4
  19P GAIN WILD-TYPE 2 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    4
  19P GAIN WILD-TYPE    2    1
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                3                  2
  MALE                  4                  1

Clustering(15) Variable = 19Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                0 1
  19Q GAIN MUTATED   4 2
  19Q GAIN WILD-TYPE 2 2
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                  4 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  2 
$`19Q GAIN 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 

$`19Q GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 
       18.08        18.05        29.23        37.15 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             10.16              18.05 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            121.25              37.15 
  19Q GAIN MUTATED 19Q GAIN 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         TCGA-OR-A5JI 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-OU-A5PI 
  "19Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-OU-A5PI 
  "19Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-OU-A5PI 
  "19Q GAIN MUTATED" 
[1] "hr=" "2.4"
D15V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  19Q GAIN MUTATED         2        1        2
  19Q GAIN WILD-TYPE       1        1        2
D15V3, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                 2                  1
  STAGE II                1                  1
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  19Q GAIN MUTATED          5
  19Q GAIN WILD-TYPE        4
[1] "NOT AVAILABLE: table dimension [2x1]"
D15V5, binary
                    cls
clus                 0 1
  19Q GAIN MUTATED   2 4
  19Q GAIN WILD-TYPE 3 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    4
  19Q GAIN WILD-TYPE    3    1
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                2                  3
  MALE                  4                  1

Clustering(16) Variable = 20P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                0 1
  20P GAIN MUTATED   2 1
  20P GAIN WILD-TYPE 4 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  7 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  3 
$`20P GAIN MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JR 
       57.53        46.78       121.25 

$`20P GAIN 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 
TCGA-OU-A5PI 
       23.31 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             46.78              10.16 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            121.25              37.15 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             57.53              18.08 
[1] "46.8 - 121.2 (57.5)" "10.2 - 37.1 (18.1)" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
"20P GAIN WILD-TYPE" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
"20P GAIN WILD-TYPE" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
"20P GAIN WILD-TYPE" 
[1] "hr="     "1.1e+09"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  20P GAIN MUTATED         2        0        0
  20P GAIN WILD-TYPE       1        2        4
D16V3, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  7 
        TCGA-OR-A5JB         TCGA-OR-A5JJ         TCGA-OR-A5JM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OR-A5JO         TCGA-OR-A5K6         TCGA-OR-A5K9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
"20P GAIN WILD-TYPE" 
                    vv
clus                 T1+T2+T4
  20P GAIN MUTATED          2
  20P GAIN WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D16V5, binary
                    cls
clus                 0 1
  20P GAIN MUTATED   0 3
  20P GAIN WILD-TYPE 5 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0    3
  20P GAIN WILD-TYPE    5    2
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                0                  5
  MALE                  3                  2

Clustering(17) Variable = 20Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                0 1
  20Q GAIN MUTATED   4 1
  20Q GAIN WILD-TYPE 2 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                  5 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  3 
$`20Q GAIN 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 

$`20Q GAIN 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 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             10.16              11.31 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            121.25              37.15 
  20Q GAIN MUTATED 20Q GAIN 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         TCGA-OR-A5JI 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "20Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "20Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-OU-A5PI 
  "20Q GAIN MUTATED" 
[1] "hr="     "1.7e+09"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  20Q GAIN MUTATED         2        0        2
  20Q GAIN WILD-TYPE       1        2        2
D17V3, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 2                  1
  STAGE II                0                  2
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  20Q GAIN MUTATED          4
  20Q GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D17V5, binary
                    cls
clus                 0 1
  20Q GAIN MUTATED   1 4
  20Q GAIN WILD-TYPE 4 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1    4
  20Q GAIN WILD-TYPE    4    1
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                1                  4
  MALE                  4                  1

Clustering(18) Variable = 21Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                0 1
  21Q GAIN MUTATED   3 2
  21Q GAIN WILD-TYPE 3 2
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                  5 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  2 
$`21Q GAIN MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5K9 TCGA-OU-A5PI 
       57.53        46.78        10.16        11.31        23.31 

$`21Q GAIN WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       18.08        18.05        29.23       121.25        37.15 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             10.16              18.05 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             57.53             121.25 
  21Q GAIN MUTATED 21Q GAIN 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         TCGA-OR-A5JI 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-OU-A5PI 
  "21Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-OU-A5PI 
  "21Q GAIN MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-OU-A5PI 
  "21Q GAIN MUTATED" 
[1] "hr=" "1.3"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  21Q GAIN MUTATED         1        1        2
  21Q GAIN WILD-TYPE       2        1        2
D18V3, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 1                  2
  STAGE II                1                  1
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  21Q GAIN MUTATED          4
  21Q GAIN WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D18V5, binary
                    cls
clus                 0 1
  21Q GAIN MUTATED   2 3
  21Q GAIN WILD-TYPE 3 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    3
  21Q GAIN WILD-TYPE    3    2
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                2                  3
  MALE                  3                  2

Clustering(19) Variable = 1P LOSS MUTATION ANALYSIS
D19V1, survival
                   sevent
clus2               0 1
  1P LOSS MUTATED   3 2
  1P LOSS WILD-TYPE 3 2
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                 5 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                 2 
$`1P LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OU-A5PI 
       57.53        46.78        18.05        37.15        23.31 

$`1P LOSS WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K9 
       18.08        10.16        29.23       121.25        11.31 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            18.05             10.16 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            57.53            121.25 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            37.15             18.08 
[1] "18.1 - 57.5 (37.1)"  "10.2 - 121.2 (18.1)"
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
[1] "hr=" "1.3"
D19V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  1P LOSS MUTATED         1        1        2
  1P LOSS WILD-TYPE       2        1        2
D19V3, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                1                 2
  STAGE II               1                 1
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  1P LOSS MUTATED          4
  1P LOSS WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D19V5, binary
                   cls
clus                0 1
  1P LOSS MUTATED   3 2
  1P LOSS WILD-TYPE 2 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    2
  1P LOSS WILD-TYPE    2    3
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               3                 2
  MALE                 2                 3

Clustering(20) Variable = 1Q LOSS MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2               0 1
  1Q LOSS MUTATED   2 2
  1Q LOSS WILD-TYPE 4 2
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                 6 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                 2 
$`1Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OU-A5PI 
       57.53        46.78        18.05        23.31 

$`1Q LOSS WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        10.16        29.23       121.25        37.15        11.31 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            18.05             10.16 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            57.53            121.25 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           35.045            23.655 
[1] "18.1 - 57.5 (35.0)"  "10.2 - 121.2 (23.7)"
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
[1] "hr=" "1.1"
D20V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  1Q LOSS MUTATED         1        0        2
  1Q LOSS WILD-TYPE       2        2        2
D20V3, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                1                 2
  STAGE II               0                 2
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  1Q LOSS MUTATED          3
  1Q LOSS WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D20V5, binary
                   cls
clus                0 1
  1Q LOSS MUTATED   2 2
  1Q LOSS WILD-TYPE 3 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    2
  1Q LOSS WILD-TYPE    3    3
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                 3
  MALE                 2                 3

Clustering(21) Variable = 3P LOSS MUTATION ANALYSIS
D21V1, survival
                   sevent
clus2               0 1
  3P LOSS MUTATED   0 3
  3P LOSS WILD-TYPE 6 1
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                 7 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                 1 
$`3P LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5K9 
       18.08        57.53        11.31 

$`3P LOSS 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 
TCGA-OU-A5PI 
       23.31 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            11.31             10.16 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            57.53            121.25 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            18.08             29.23 
[1] "11.3 - 57.5 (18.1)"  "10.2 - 121.2 (29.2)"
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
[1] "hr=" "6.2"
D21V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  3P LOSS MUTATED         0        1        1
  3P LOSS WILD-TYPE       3        1        3
D21V3, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 7 
       TCGA-OR-A5JI        TCGA-OR-A5JJ        TCGA-OR-A5JM        TCGA-OR-A5JO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-OR-A5JR        TCGA-OR-A5K6        TCGA-OU-A5PI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                T1+T2+T4
  3P LOSS MUTATED          2
  3P LOSS WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D21V5, binary
                   cls
clus                0 1
  3P LOSS MUTATED   1 2
  3P LOSS WILD-TYPE 4 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    2
  3P LOSS WILD-TYPE    4    3
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               1                 4
  MALE                 2                 3

Clustering(22) Variable = 8P LOSS MUTATION ANALYSIS
D22V1, survival
                   sevent
clus2               0 1
  8P LOSS MUTATED   2 1
  8P LOSS WILD-TYPE 4 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                 7 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 3 
$`8P LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5K6 TCGA-OU-A5PI 
       18.08        37.15        23.31 

$`8P LOSS WILD-TYPE`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR 
       57.53        46.78        10.16        18.05        29.23       121.25 
TCGA-OR-A5K9 
       11.31 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            18.08             10.16 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            37.15            121.25 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            23.31             29.23 
[1] "18.1 - 37.1 (23.3)"  "10.2 - 121.2 (29.2)"
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
[1] "hr=" "1.2"
D22V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  8P LOSS MUTATED         0        1        2
  8P LOSS WILD-TYPE       3        1        2
D22V3, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                0                 3
  STAGE II               1                 1
  STAGE IV               2                 2
                   vv
clus                T1+T2+T4
  8P LOSS MUTATED          3
  8P LOSS WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D22V5, binary
                   cls
clus                0 1
  8P LOSS MUTATED   2 1
  8P LOSS WILD-TYPE 3 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    1
  8P LOSS WILD-TYPE    3    4
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               2                 3
  MALE                 1                 4

Clustering(23) Variable = 9P LOSS MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2               0 1
  9P LOSS MUTATED   1 2
  9P LOSS WILD-TYPE 5 2
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                 7 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 2 
$`9P LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OR-A5K6 
       57.53        18.05        37.15 

$`9P LOSS 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 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            18.05             10.16 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            57.53            121.25 
  9P LOSS MUTATED 9P LOSS 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        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D23V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  9P LOSS MUTATED         0        1        1
  9P LOSS WILD-TYPE       3        1        3
D23V3, multiclass
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 7 
       TCGA-OR-A5JB        TCGA-OR-A5JI        TCGA-OR-A5JJ        TCGA-OR-A5JO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-OR-A5JR        TCGA-OR-A5K9        TCGA-OU-A5PI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
                   vv
clus                T1+T2+T4
  9P LOSS MUTATED          2
  9P LOSS WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D23V5, binary
                   cls
clus                0 1
  9P LOSS MUTATED   2 1
  9P LOSS WILD-TYPE 3 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    1
  9P LOSS WILD-TYPE    3    4
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               2                 3
  MALE                 1                 4

Clustering(24) Variable = 9Q LOSS MUTATION ANALYSIS
D24V1, survival
                   sevent
clus2               0 1
  9Q LOSS MUTATED   1 2
  9Q LOSS WILD-TYPE 5 2
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                 7 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 2 
$`9Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OR-A5K6 
       57.53        18.05        37.15 

$`9Q LOSS 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 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            18.05             10.16 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            57.53            121.25 
  9Q LOSS MUTATED 9Q LOSS 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        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D24V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  9Q LOSS MUTATED         0        1        1
  9Q LOSS WILD-TYPE       3        1        3
D24V3, multiclass
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 7 
       TCGA-OR-A5JB        TCGA-OR-A5JI        TCGA-OR-A5JJ        TCGA-OR-A5JO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-OR-A5JR        TCGA-OR-A5K9        TCGA-OU-A5PI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
                   vv
clus                T1+T2+T4
  9Q LOSS MUTATED          2
  9Q LOSS WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D24V5, binary
                   cls
clus                0 1
  9Q LOSS MUTATED   2 1
  9Q LOSS WILD-TYPE 3 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2    1
  9Q LOSS WILD-TYPE    3    4
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               2                 3
  MALE                 1                 4

Clustering(25) Variable = 11P LOSS MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                0 1
  11P LOSS MUTATED   3 2
  11P LOSS WILD-TYPE 3 2
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  5 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                  2 
$`11P LOSS 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 

$`11P LOSS 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 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             11.31              10.16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             57.53             121.25 
  11P LOSS MUTATED 11P LOSS 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         TCGA-OR-A5JI 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-OU-A5PI 
  "11P LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-OU-A5PI 
  "11P LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-OU-A5PI 
  "11P LOSS MUTATED" 
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  11P LOSS MUTATED         1        2        1
  11P LOSS WILD-TYPE       2        0        3
D25V3, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                 1                  2
  STAGE II                2                  0
  STAGE IV                1                  3
                    vv
clus                 T1+T2+T4
  11P LOSS MUTATED          4
  11P LOSS WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D25V5, binary
                    cls
clus                 0 1
  11P LOSS MUTATED   3 2
  11P LOSS WILD-TYPE 2 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    2
  11P LOSS WILD-TYPE    2    3
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                3                  2
  MALE                  2                  3

Clustering(26) Variable = 11Q LOSS MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                0 1
  11Q LOSS MUTATED   3 2
  11Q LOSS WILD-TYPE 3 2
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  5 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                  2 
$`11Q LOSS 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 

$`11Q LOSS 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 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             11.31              10.16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             57.53             121.25 
  11Q LOSS MUTATED 11Q LOSS 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         TCGA-OR-A5JI 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "11Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "11Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "11Q LOSS MUTATED" 
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  11Q LOSS MUTATED         1        2        1
  11Q LOSS WILD-TYPE       2        0        3
D26V3, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                 1                  2
  STAGE II                2                  0
  STAGE IV                1                  3
                    vv
clus                 T1+T2+T4
  11Q LOSS MUTATED          4
  11Q LOSS WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D26V5, binary
                    cls
clus                 0 1
  11Q LOSS MUTATED   3 2
  11Q LOSS WILD-TYPE 2 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    2
  11Q LOSS WILD-TYPE    2    3
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                3                  2
  MALE                  2                  3

Clustering(27) Variable = 13Q LOSS MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                0 1
  13Q LOSS MUTATED   2 3
  13Q LOSS WILD-TYPE 4 1
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                  5 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                  1 
$`13Q LOSS 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 

$`13Q LOSS 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 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             11.31              10.16 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             57.53             121.25 
  13Q LOSS MUTATED 13Q LOSS 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         TCGA-OR-A5JI 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "13Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "13Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "13Q LOSS MUTATED" 
[1] "hr=" "2.7"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  13Q LOSS MUTATED         1        1        2
  13Q LOSS WILD-TYPE       2        1        2
D27V3, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 1                  2
  STAGE II                1                  1
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  13Q LOSS MUTATED          4
  13Q LOSS WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D27V5, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   2 3
  13Q LOSS WILD-TYPE 3 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    3
  13Q LOSS WILD-TYPE    3    2
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                  3
  MALE                  3                  2

Clustering(28) Variable = 15Q LOSS MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                0 1
  15Q LOSS MUTATED   2 2
  15Q LOSS WILD-TYPE 4 2
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                  6 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                  2 
$`15Q LOSS MUTATED`
TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5K9 TCGA-OU-A5PI 
       46.78        18.05        11.31        23.31 

$`15Q LOSS WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       18.08        57.53        10.16        29.23       121.25        37.15 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             11.31              10.16 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             46.78             121.25 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             20.68              33.19 
[1] "11.3 - 46.8 (20.7)"  "10.2 - 121.2 (33.2)"
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "15Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "15Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "15Q LOSS MUTATED" 
[1] "hr=" "3.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  15Q LOSS MUTATED         1        1        2
  15Q LOSS WILD-TYPE       2        1        2
D28V3, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                 1                  2
  STAGE II                1                  1
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  15Q LOSS MUTATED          4
  15Q LOSS WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D28V5, binary
                    cls
clus                 0 1
  15Q LOSS MUTATED   3 1
  15Q LOSS WILD-TYPE 2 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    1
  15Q LOSS WILD-TYPE    2    4
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                3                  2
  MALE                  1                  4

Clustering(29) Variable = 17P LOSS MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                0 1
  17P LOSS MUTATED   1 4
  17P LOSS WILD-TYPE 5 0
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                  5 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                  0 
$`17P LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JM TCGA-OR-A5K9 TCGA-OU-A5PI 
       18.08        57.53        18.05        11.31        23.31 

$`17P LOSS WILD-TYPE`
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 
       46.78        10.16        29.23       121.25        37.15 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             11.31              10.16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             57.53             121.25 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             18.08              37.15 
[1] "11.3 - 57.5 (18.1)"  "10.2 - 121.2 (37.1)"
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-OU-A5PI 
  "17P LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-OU-A5PI 
  "17P LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-OU-A5PI 
  "17P LOSS MUTATED" 
[1] "hr="     "1.7e+09"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  17P LOSS MUTATED         0        1        3
  17P LOSS WILD-TYPE       3        1        1
D29V3, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 0                  3
  STAGE II                1                  1
  STAGE IV                3                  1
                    vv
clus                 T1+T2+T4
  17P LOSS MUTATED          4
  17P LOSS WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D29V5, binary
                    cls
clus                 0 1
  17P LOSS MUTATED   3 2
  17P LOSS WILD-TYPE 2 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    2
  17P LOSS WILD-TYPE    2    3
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                3                  2
  MALE                  2                  3

Clustering(30) Variable = 17Q LOSS MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                0 1
  17Q LOSS MUTATED   1 2
  17Q LOSS WILD-TYPE 5 2
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                  7 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                  2 
$`17Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5K9 TCGA-OU-A5PI 
       57.53        11.31        23.31 

$`17Q LOSS 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 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             11.31              10.16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             57.53             121.25 
  17Q LOSS MUTATED 17Q LOSS 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         TCGA-OR-A5JI 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "17Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "17Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "17Q LOSS MUTATED" 
[1] "hr=" "2"  
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  17Q LOSS MUTATED         0        1        1
  17Q LOSS WILD-TYPE       3        1        3
D30V3, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                  7 
        TCGA-OR-A5JB         TCGA-OR-A5JI         TCGA-OR-A5JJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5JM         TCGA-OR-A5JO         TCGA-OR-A5JR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-OR-A5K6 
"17Q LOSS WILD-TYPE" 
                    vv
clus                 T1+T2+T4
  17Q LOSS MUTATED          2
  17Q LOSS WILD-TYPE        7
[1] "NOT AVAILABLE: table dimension [2x1]"
D30V5, binary
                    cls
clus                 0 1
  17Q LOSS MUTATED   2 1
  17Q LOSS WILD-TYPE 3 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    1
  17Q LOSS WILD-TYPE    3    4
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                  3
  MALE                  1                  4

Clustering(31) Variable = 18P LOSS MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                0 1
  18P LOSS MUTATED   2 2
  18P LOSS WILD-TYPE 4 2
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  6 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  2 
$`18P LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OU-A5PI 
       18.08        57.53        46.78        23.31 

$`18P LOSS WILD-TYPE`
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 
       10.16        18.05        29.23       121.25        37.15        11.31 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             18.08              10.16 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             57.53             121.25 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            35.045             23.640 
[1] "18.1 - 57.5 (35.0)"  "10.2 - 121.2 (23.6)"
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-OU-A5PI 
  "18P LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-OU-A5PI 
  "18P LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-OU-A5PI 
  "18P LOSS MUTATED" 
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  18P LOSS MUTATED         1        0        2
  18P LOSS WILD-TYPE       2        2        2
D31V3, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 1                  2
  STAGE II                0                  2
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  18P LOSS MUTATED          3
  18P LOSS WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D31V5, binary
                    cls
clus                 0 1
  18P LOSS MUTATED   1 3
  18P LOSS WILD-TYPE 4 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    3
  18P LOSS WILD-TYPE    4    2
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                1                  4
  MALE                  3                  2

Clustering(32) Variable = 18Q LOSS MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                0 1
  18Q LOSS MUTATED   2 2
  18Q LOSS WILD-TYPE 4 2
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                  6 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  2 
$`18Q LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OU-A5PI 
       18.08        57.53        46.78        23.31 

$`18Q LOSS WILD-TYPE`
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 
       10.16        18.05        29.23       121.25        37.15        11.31 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             18.08              10.16 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             57.53             121.25 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            35.045             23.640 
[1] "18.1 - 57.5 (35.0)"  "10.2 - 121.2 (23.6)"
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-OU-A5PI 
  "18Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-OU-A5PI 
  "18Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-OU-A5PI 
  "18Q LOSS MUTATED" 
[1] "hr=" "1"  
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  18Q LOSS MUTATED         1        0        2
  18Q LOSS WILD-TYPE       2        2        2
D32V3, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 1                  2
  STAGE II                0                  2
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  18Q LOSS MUTATED          3
  18Q LOSS WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D32V5, binary
                    cls
clus                 0 1
  18Q LOSS MUTATED   1 3
  18Q LOSS WILD-TYPE 4 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE    4    2
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                1                  4
  MALE                  3                  2

Clustering(33) Variable = 22Q LOSS MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                0 1
  22Q LOSS MUTATED   3 3
  22Q LOSS WILD-TYPE 3 1
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 6                  4 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                  1 
$`22Q LOSS 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 

$`22Q LOSS WILD-TYPE`
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5K6 
       10.16        18.05        29.23        37.15 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             11.31              10.16 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            121.25              37.15 
  22Q LOSS MUTATED 22Q LOSS 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         TCGA-OR-A5JI 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "22Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "22Q LOSS MUTATED" 
        TCGA-OR-A5JB         TCGA-OR-A5JC         TCGA-OR-A5JI 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-OR-A5JJ         TCGA-OR-A5JM         TCGA-OR-A5JO 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-OR-A5JR         TCGA-OR-A5K6         TCGA-OR-A5K9 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-OU-A5PI 
  "22Q LOSS MUTATED" 
[1] "hr=" "1"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IV
  22Q LOSS MUTATED         2        1        2
  22Q LOSS WILD-TYPE       1        1        2
D33V3, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 2                  1
  STAGE II                1                  1
  STAGE IV                2                  2
                    vv
clus                 T1+T2+T4
  22Q LOSS MUTATED          5
  22Q LOSS WILD-TYPE        4
[1] "NOT AVAILABLE: table dimension [2x1]"
D33V5, binary
                    cls
clus                 0 1
  22Q LOSS MUTATED   2 4
  22Q LOSS WILD-TYPE 3 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2    4
  22Q LOSS WILD-TYPE    3    1
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                2                  3
  MALE                  4                  1

Clustering(34) Variable = XQ LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2               0 1
  XQ LOSS MUTATED   1 2
  XQ LOSS WILD-TYPE 5 2
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                 7 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                 2 
$`XQ LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        37.15        11.31 

$`XQ LOSS WILD-TYPE`
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR 
       57.53        46.78        10.16        18.05        29.23       121.25 
TCGA-OU-A5PI 
       23.31 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            11.31             10.16 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            37.15            121.25 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            18.08             29.23 
[1] "11.3 - 37.1 (18.1)"  "10.2 - 121.2 (29.2)"
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-OR-A5JB        TCGA-OR-A5JC        TCGA-OR-A5JI        TCGA-OR-A5JJ 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-OR-A5JM        TCGA-OR-A5JO        TCGA-OR-A5JR        TCGA-OR-A5K6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-OR-A5K9        TCGA-OU-A5PI 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
[1] "hr=" "5"  
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IV
  XQ LOSS MUTATED         0        2        1
  XQ LOSS WILD-TYPE       3        0        3
D34V3, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                0                 3
  STAGE II               2                 0
  STAGE IV               1                 3
                   vv
clus                T1+T2+T4
  XQ LOSS MUTATED          3
  XQ LOSS WILD-TYPE        6
[1] "NOT AVAILABLE: table dimension [2x1]"
D34V5, binary
                   cls
clus                0 1
  XQ LOSS MUTATED   2 1
  XQ LOSS WILD-TYPE 3 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    1
  XQ LOSS WILD-TYPE    3    4
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                 3
  MALE                 1                 4
> q(save="no")
