
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/KICH-TP/4466672/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/4434596/KICH-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KICH-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=KICH-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/4434596/KICH-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/4466672/transformed.cor.cli.txt"

nPatients in clinical file=64, in cluster file=66, common to both=64
[1] "Reduce the number of clustering variables from 80 to 59."
[1] 59 64
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8                56 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8                56 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                56 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                56 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19                45 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19                45 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18                46 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18                46 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                57 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                57 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                57 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                57 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               23                41 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               23                41 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               23                41 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               23                41 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               15                49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               15                49 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               16                48 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               16                48 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                54 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                54 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                54 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                54 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                14                 50 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                14                 50 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                 49 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                 49 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                 47 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                17                 47 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                 47 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                 47 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                17                 47 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                17                 47 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                18                 46 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                18                 46 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                18                 46 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                18                 46 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                 46 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                 46 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 50 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 50 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 51 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 51 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                17                 47 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                17                 47 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                 48 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                 48 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                18                 46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                18                 46 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                18                 46 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                18                 46 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 61 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 61 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 47 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 47 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               10                54 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               10                54 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               47                17 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               47                17 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47                17 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47                17 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               42                22 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               42                22 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               42                22 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               42                22 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                57 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                57 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                58 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                58 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                58 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                58 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                58 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                58 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               46                18 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               46                18 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47                17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47                17 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                54 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                54 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                55 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                55 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                58 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                58 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                57 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                57 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 19 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 19 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 19 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 19 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 57 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 57 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 57 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 57 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                 24 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                 24 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 60 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 60 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 59 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 59 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                 18 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                 18 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                 18 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                 18 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 58 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 58 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 56 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 56 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 60 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 60 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 61 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 61 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                 32 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                 32 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 56 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 56 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               40                24 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               40                24 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "NEOPLASM.DISEASESTAGE"           
 [7] "PATHOLOGY.T.STAGE"                "PATHOLOGY.N.STAGE"               
 [9] "PATHOLOGY.M.STAGE"                "DCCUPLOADDATE"                   
[11] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
[13] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[15] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[17] "YEAROFTOBACCOSMOKINGONSET"        "BATCHNUMBER"                     

Input Data has 18 rows and 64 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
          NA         3321         4169         3126         2752         3304 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
        3009         2582         2990         2949         2815           NA 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
        1364         2632           NA         2024           NA         2248 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
        1815          876         1664         1896         4621          247 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
         994          400         1082         1128         3745         1552 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
         953         3473          714         2674          775          788 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
        1983         2211          107           17           NA         2063 
TCGA-KN-8430 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
          NA          712           76          341         1124         2727 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
         636         2303         2339           NA         2279         2404 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
        2820           NA         2445         2670         3141         2618 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        2368         1739         1873         1944 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
[3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
[5] "PATHOLOGY.M.STAGE"           "GENDER"                     
[7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
[9] "YEAROFTOBACCOSMOKINGONSET"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 64 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
21 23 18  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   21    23    20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
21 23 18  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   21    23    20 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
40  3  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   40     5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
40  3  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 40

$Class1_nSamples
[1] 5

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   40     5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=9, binary=FALSE, numeric=TRUE
YEAROFTOBACCOSMOKINGONSET, nv=8, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 3P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  3
  3P GAIN WILD-TYPE 52  4
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7                56 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                 4 
$`3P GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 
       98.93        28.08        24.79        62.33        37.08         0.56 
TCGA-KN-8428 
       52.27 

$`3P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.53        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
      151.92         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.02        31.33       114.18        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19        72.69         3.52        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        36.95        89.65        20.91        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.07        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.56              2.50 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            98.93            151.92 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            37.08             67.18 
[1] "0.6 - 98.9 (37.1)"  "2.5 - 151.9 (67.2)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "7.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         1        4         0        3
  3P GAIN WILD-TYPE      20       19        14        3
D1V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                4                19
  STAGE III               0                14
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  3P GAIN MUTATED    1  4     3
  3P GAIN WILD-TYPE 20 19    17
D1V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                  1                20
  T2                  4                19
  T3+T4               3                17
                   vv
clus                N0 N1+N2
  3P GAIN MUTATED    5     3
  3P GAIN WILD-TYPE 35     2
D1V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                  5                35
  N1+N2               3                 2
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED    3  1  1
  3P GAIN WILD-TYPE 29  1  8
D1V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               3                29
  M1               1                 1
  MX               1                 8
D1V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  7
  3P GAIN WILD-TYPE 24 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    7
  3P GAIN WILD-TYPE   24   32
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                24
  MALE                 7                32
D1V8, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                10 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KO-8411        TCGA-KO-8413 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D1V9, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 8 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D1V10, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 

Clustering(2) Variable = 3Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4  3
  3Q GAIN WILD-TYPE 52  4
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                56 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                 4 
$`3Q GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 
       98.93        28.08        24.79        62.33        37.08         0.56 
TCGA-KN-8428 
       52.27 

$`3Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.53        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
      151.92         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.02        31.33       114.18        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19        72.69         3.52        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        36.95        89.65        20.91        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.07        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.56              2.50 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            98.93            151.92 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            37.08             67.18 
[1] "0.6 - 98.9 (37.1)"  "2.5 - 151.9 (67.2)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "7.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         1        4         0        3
  3Q GAIN WILD-TYPE      20       19        14        3
D2V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                4                19
  STAGE III               0                14
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  3Q GAIN MUTATED    1  4     3
  3Q GAIN WILD-TYPE 20 19    17
D2V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                  1                20
  T2                  4                19
  T3+T4               3                17
                   vv
clus                N0 N1+N2
  3Q GAIN MUTATED    5     3
  3Q GAIN WILD-TYPE 35     2
D2V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                  5                35
  N1+N2               3                 2
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED    3  1  1
  3Q GAIN WILD-TYPE 29  1  8
D2V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               3                29
  M1               1                 1
  MX               1                 8
D2V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    1  7
  3Q GAIN WILD-TYPE 24 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    7
  3Q GAIN WILD-TYPE   24   32
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               1                24
  MALE                 7                32
D2V8, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                10 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KO-8411        TCGA-KO-8413 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D2V9, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 8 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D2V10, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 

Clustering(3) Variable = 4P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   15  3
  4P GAIN WILD-TYPE 41  4
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18                45 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                 4 
$`4P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        28.08        24.79        62.33       151.92        37.08 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 
       23.47        25.48        25.91        72.69         3.52        11.21 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       10.68        74.93        80.38        87.78        86.07        77.85 

$`4P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.53        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 
       31.33       114.18        87.91        65.19         0.56        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       75.72        76.90        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.91 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             3.52              0.56 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           151.92            123.12 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           49.705            65.190 
[1] "3.5 - 151.9 (49.7)" "0.6 - 123.1 (65.2)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED"   "4P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         7        6         2        4
  4P GAIN WILD-TYPE      14       17        12        2
D3V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 7                14
  STAGE II                6                17
  STAGE III               2                12
  STAGE IV                4                 2
                   vv
clus                T1 T2 T3+T4
  4P GAIN MUTATED    7  6     6
  4P GAIN WILD-TYPE 14 17    14
D3V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  7                14
  T2                  6                17
  T3+T4               6                14
                   vv
clus                N0 N1+N2
  4P GAIN MUTATED   14     2
  4P GAIN WILD-TYPE 26     3
D3V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                 14                26
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    8  2  2
  4P GAIN WILD-TYPE 24  0  7
D3V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               8                24
  M1               2                 0
  MX               2                 7
D3V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    6 13
  4P GAIN WILD-TYPE 19 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6   13
  4P GAIN WILD-TYPE   19   26
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6                19
  MALE                13                26
D3V8, continuous
D3V9, continuous
D3V10, continuous

Clustering(4) Variable = 4Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   15  3
  4Q GAIN WILD-TYPE 41  4
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18                45 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                 4 
$`4Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        28.08        24.79        62.33       151.92        37.08 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 
       23.47        25.48        25.91        72.69         3.52        11.21 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       10.68        74.93        80.38        87.78        86.07        77.85 

$`4Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.53        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 
       31.33       114.18        87.91        65.19         0.56        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       75.72        76.90        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.91 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.52              0.56 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           151.92            123.12 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           49.705            65.190 
[1] "3.5 - 151.9 (49.7)" "0.6 - 123.1 (65.2)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED"   "4Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         6        6         2        4
  4Q GAIN WILD-TYPE      15       17        12        2
D4V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 6                15
  STAGE II                6                17
  STAGE III               2                12
  STAGE IV                4                 2
                   vv
clus                T1 T2 T3+T4
  4Q GAIN MUTATED    6  6     6
  4Q GAIN WILD-TYPE 15 17    14
D4V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  6                15
  T2                  6                17
  T3+T4               6                14
                   vv
clus                N0 N1+N2
  4Q GAIN MUTATED   13     2
  4Q GAIN WILD-TYPE 27     3
D4V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0                 13                27
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  4Q GAIN MUTATED    8  2  2
  4Q GAIN WILD-TYPE 24  0  7
D4V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               8                24
  M1               2                 0
  MX               2                 7
D4V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    6 12
  4Q GAIN WILD-TYPE 19 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6   12
  4Q GAIN WILD-TYPE   19   27
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               6                19
  MALE                12                27
D4V8, continuous
D4V9, continuous
D4V10, continuous

Clustering(5) Variable = 5P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    4  3
  5P GAIN WILD-TYPE 52  4
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                56 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                 4 
$`5P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8404 
      137.06        28.08         3.52         0.56        52.27        10.68 
TCGA-KO-8414 
       77.85 

$`5P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       35.57        37.08       123.12        51.02        31.33       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19        72.69 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       67.82        23.41         2.50        11.21        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       16.67        80.38        87.78       103.27        86.07        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.56              2.50 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           137.06            151.92 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           28.080            65.865 
[1] "0.6 - 137.1 (28.1)" "2.5 - 151.9 (65.9)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "9.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         1        2         0        4
  5P GAIN WILD-TYPE      20       21        14        2
D5V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                2                21
  STAGE III               0                14
  STAGE IV                4                 2
                   vv
clus                T1 T2 T3+T4
  5P GAIN MUTATED    1  2     4
  5P GAIN WILD-TYPE 20 21    16
D5V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                  1                20
  T2                  2                21
  T3+T4               4                16
                   vv
clus                N0 N1+N2
  5P GAIN MUTATED    3     2
  5P GAIN WILD-TYPE 37     3
D5V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                  3                37
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED    2  2  0
  5P GAIN WILD-TYPE 30  0  9
D5V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               2                30
  M1               2                 0
  MX               0                 9
D5V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  5
  5P GAIN WILD-TYPE 23 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    5
  5P GAIN WILD-TYPE   23   34
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                23
  MALE                 5                34
D5V8, continuous
D5V9, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-KO-8416 
"5P GAIN WILD-TYPE" 
D5V10, continuous

Clustering(6) Variable = 5Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    4  3
  5Q GAIN WILD-TYPE 52  4
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                56 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                 4 
$`5Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8404 
      137.06        28.08         3.52         0.56        52.27        10.68 
TCGA-KO-8414 
       77.85 

$`5Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       35.57        37.08       123.12        51.02        31.33       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19        72.69 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       67.82        23.41         2.50        11.21        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       16.67        80.38        87.78       103.27        86.07        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.56              2.50 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           137.06            151.92 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           28.080            65.865 
[1] "0.6 - 137.1 (28.1)" "2.5 - 151.9 (65.9)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr=" "9.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         1        2         0        4
  5Q GAIN WILD-TYPE      20       21        14        2
D6V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                2                21
  STAGE III               0                14
  STAGE IV                4                 2
                   vv
clus                T1 T2 T3+T4
  5Q GAIN MUTATED    1  2     4
  5Q GAIN WILD-TYPE 20 21    16
D6V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                  1                20
  T2                  2                21
  T3+T4               4                16
                   vv
clus                N0 N1+N2
  5Q GAIN MUTATED    3     2
  5Q GAIN WILD-TYPE 37     3
D6V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                  3                37
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED    2  2  0
  5Q GAIN WILD-TYPE 30  0  9
D6V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               2                30
  M1               2                 0
  MX               0                 9
D6V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  5
  5Q GAIN WILD-TYPE 23 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    5
  5Q GAIN WILD-TYPE   23   34
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                23
  MALE                 5                34
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-KO-8416 
"5Q GAIN WILD-TYPE" 
D6V10, continuous

Clustering(7) Variable = 7P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   17  5
  7P GAIN WILD-TYPE 39  2
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22                41 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                 2 
$`7P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8346 
      137.06        98.93        28.08        24.79        59.67        62.33 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      151.92        37.08        23.47        25.91        72.69         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8408 
        0.56        52.27        11.21        10.68        74.93        16.67 
TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        86.07        77.85        57.17 

$`7P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 
       66.54        73.91        28.80        54.71         8.12        32.68 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       13.15        35.57       123.12        51.02        31.33       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       87.91        25.48        65.19        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 
       36.95        89.65        20.91        75.72        76.90        79.04 
TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       92.71        87.78       103.27        61.58        63.91 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.56              2.50 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           151.92            123.12 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            54.72             67.82 
[1] "0.6 - 151.9 (54.7)" "2.5 - 123.1 (67.8)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
[1] "hr=" "5.7"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         6        8         4        5
  7P GAIN WILD-TYPE      15       15        10        1
D7V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 6                15
  STAGE II                8                15
  STAGE III               4                10
  STAGE IV                5                 1
                   vv
clus                T1 T2 T3+T4
  7P GAIN MUTATED    6  8     9
  7P GAIN WILD-TYPE 15 15    11
D7V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                  6                15
  T2                  8                15
  T3+T4               9                11
                   vv
clus                N0 N1+N2
  7P GAIN MUTATED   16     4
  7P GAIN WILD-TYPE 24     1
D7V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                 16                24
  N1+N2               4                 1
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   10  2  2
  7P GAIN WILD-TYPE 22  0  7
D7V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              10                22
  M1               2                 0
  MX               2                 7
D7V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6 17
  7P GAIN WILD-TYPE 19 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   17
  7P GAIN WILD-TYPE   19   22
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               6                19
  MALE                17                22
D7V8, continuous
D7V9, continuous
D7V10, continuous

Clustering(8) Variable = 7Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   17  5
  7Q GAIN WILD-TYPE 39  2
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22                41 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                 2 
$`7Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8346 
      137.06        98.93        28.08        24.79        59.67        62.33 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      151.92        37.08        23.47        25.91        72.69         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8408 
        0.56        52.27        11.21        10.68        74.93        16.67 
TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        86.07        77.85        57.17 

$`7Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 
       66.54        73.91        28.80        54.71         8.12        32.68 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       13.15        35.57       123.12        51.02        31.33       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       87.91        25.48        65.19        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 
       36.95        89.65        20.91        75.72        76.90        79.04 
TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       92.71        87.78       103.27        61.58        63.91 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.56              2.50 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           151.92            123.12 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            54.72             67.82 
[1] "0.6 - 151.9 (54.7)" "2.5 - 123.1 (67.8)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
[1] "hr=" "5.7"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         6        8         4        5
  7Q GAIN WILD-TYPE      15       15        10        1
D8V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 6                15
  STAGE II                8                15
  STAGE III               4                10
  STAGE IV                5                 1
                   vv
clus                T1 T2 T3+T4
  7Q GAIN MUTATED    6  8     9
  7Q GAIN WILD-TYPE 15 15    11
D8V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                  6                15
  T2                  8                15
  T3+T4               9                11
                   vv
clus                N0 N1+N2
  7Q GAIN MUTATED   16     4
  7Q GAIN WILD-TYPE 24     1
D8V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                 16                24
  N1+N2               4                 1
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   10  2  2
  7Q GAIN WILD-TYPE 22  0  7
D8V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              10                22
  M1               2                 0
  MX               2                 7
D8V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    6 17
  7Q GAIN WILD-TYPE 19 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6   17
  7Q GAIN WILD-TYPE   19   22
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               6                19
  MALE                17                22
D8V8, continuous
D8V9, continuous
D8V10, continuous

Clustering(9) Variable = 8P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   12  2
  8P GAIN WILD-TYPE 44  5
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               14                49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 5 
$`8P GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
       98.93        28.08        62.33       151.92        37.08        23.47 
TCGA-KN-8423 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 
       25.91         0.56        52.27        11.21        74.93        80.38 
TCGA-KO-8410 TCGA-KO-8413 
       87.78        86.07 

$`8P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.71         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.02        31.33       114.18        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       72.69         3.52        67.82        23.41         2.50        36.95 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
       89.65        20.91        75.72        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       103.27        77.85        57.17        61.58 
TCGA-KO-8417 
       63.91 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.56              2.50 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           151.92            137.06 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            57.30             65.19 
[1] "0.6 - 151.9 (57.3)" "2.5 - 137.1 (65.2)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         4        7         2        2
  8P GAIN WILD-TYPE      17       16        12        4
D9V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 4                17
  STAGE II                7                16
  STAGE III               2                12
  STAGE IV                2                 4
                   vv
clus                T1 T2 T3+T4
  8P GAIN MUTATED    4  7     4
  8P GAIN WILD-TYPE 17 16    16
D9V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  4                17
  T2                  7                16
  T3+T4               4                16
                   vv
clus                N0 N1+N2
  8P GAIN MUTATED   12     2
  8P GAIN WILD-TYPE 28     3
D9V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 12                28
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED    6  1  2
  8P GAIN WILD-TYPE 26  1  7
D9V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               6                26
  M1               1                 1
  MX               2                 7
D9V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4 11
  8P GAIN WILD-TYPE 21 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   11
  8P GAIN WILD-TYPE   21   28
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                21
  MALE                11                28
D9V8, continuous
D9V9, continuous
D9V10, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8408 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 

Clustering(10) Variable = 8Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   13  2
  8Q GAIN WILD-TYPE 43  5
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               15                48 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 5 
$`8Q GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
       98.93        28.08        62.33       151.92        37.08        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8405 
       25.91         3.52         0.56        52.27        11.21        74.93 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       80.38        87.78        86.07 

$`8Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.71         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.02        31.33       114.18        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       72.69        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        77.85        57.17        61.58        63.91 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.56              2.50 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           151.92            137.06 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           52.270            65.865 
[1] "0.6 - 151.9 (52.3)" "2.5 - 137.1 (65.9)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         4        7         2        3
  8Q GAIN WILD-TYPE      17       16        12        3
D10V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 4                17
  STAGE II                7                16
  STAGE III               2                12
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  8Q GAIN MUTATED    4  7     5
  8Q GAIN WILD-TYPE 17 16    15
D10V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  4                17
  T2                  7                16
  T3+T4               5                15
                   vv
clus                N0 N1+N2
  8Q GAIN MUTATED   12     2
  8Q GAIN WILD-TYPE 28     3
D10V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                 12                28
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED    6  2  2
  8Q GAIN WILD-TYPE 26  0  7
D10V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               6                26
  M1               2                 0
  MX               2                 7
D10V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4 12
  8Q GAIN WILD-TYPE 21 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   12
  8Q GAIN WILD-TYPE   21   27
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               4                21
  MALE                12                27
D10V8, continuous
D10V9, continuous
D10V10, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8408 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 

Clustering(11) Variable = 9P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    8  2
  9P GAIN WILD-TYPE 48  5
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                53 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 5 
$`9P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8427 
      137.06        98.93        24.79       151.92        37.08         0.56 
TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 
       52.27        74.93        80.38        77.85 

$`9P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       28.08        66.54        73.91        59.67        28.80        54.71 
TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       62.33         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.02        31.33       114.18        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19        72.69         3.52        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        36.95        89.65        20.91        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 
       76.90        10.68        79.04        92.71        16.67        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.07        57.17        61.58        63.91 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.56              2.50 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           151.92            123.12 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            76.39             62.33 
[1] "0.6 - 151.9 (76.4)" "2.5 - 123.1 (62.3)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         1        6         1        2
  9P GAIN WILD-TYPE      20       17        13        4
D11V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                6                17
  STAGE III               1                13
  STAGE IV                2                 4
                   vv
clus                T1 T2 T3+T4
  9P GAIN MUTATED    1  6     3
  9P GAIN WILD-TYPE 20 17    17
D11V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                  1                20
  T2                  6                17
  T3+T4               3                17
                   vv
clus                N0 N1+N2
  9P GAIN MUTATED    8     2
  9P GAIN WILD-TYPE 32     3
D11V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0                  8                32
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  9P GAIN MUTATED    6  0  2
  9P GAIN WILD-TYPE 26  2  7
D11V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               6                26
  M1               0                 2
  MX               2                 7
D11V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    4  6
  9P GAIN WILD-TYPE 21 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    6
  9P GAIN WILD-TYPE   21   33
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               4                21
  MALE                 6                33
D11V8, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KO-8413 
"9P GAIN WILD-TYPE" 
D11V9, continuous
D11V10, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 

Clustering(12) Variable = 9Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    8  2
  9Q GAIN WILD-TYPE 48  5
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                53 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 5 
$`9Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8427 
      137.06        98.93        24.79       151.92        37.08         0.56 
TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 
       52.27        74.93        80.38        77.85 

$`9Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       28.08        66.54        73.91        59.67        28.80        54.71 
TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       62.33         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.02        31.33       114.18        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19        72.69         3.52        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        36.95        89.65        20.91        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 
       76.90        10.68        79.04        92.71        16.67        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.07        57.17        61.58        63.91 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.56              2.50 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           151.92            123.12 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            76.39             62.33 
[1] "0.6 - 151.9 (76.4)" "2.5 - 123.1 (62.3)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1        6         1        2
  9Q GAIN WILD-TYPE      20       17        13        4
D12V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                20
  STAGE II                6                17
  STAGE III               1                13
  STAGE IV                2                 4
                   vv
clus                T1 T2 T3+T4
  9Q GAIN MUTATED    1  6     3
  9Q GAIN WILD-TYPE 20 17    17
D12V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1                  1                20
  T2                  6                17
  T3+T4               3                17
                   vv
clus                N0 N1+N2
  9Q GAIN MUTATED    8     2
  9Q GAIN WILD-TYPE 32     3
D12V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                  8                32
  N1+N2               2                 3
                   vv
clus                M0 M1 MX
  9Q GAIN MUTATED    6  0  2
  9Q GAIN WILD-TYPE 26  2  7
D12V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               6                26
  M1               0                 2
  MX               2                 7
D12V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  6
  9Q GAIN WILD-TYPE 21 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    6
  9Q GAIN WILD-TYPE   21   33
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               4                21
  MALE                 6                33
D12V8, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KO-8413 
"9Q GAIN WILD-TYPE" 
D12V9, continuous
D12V10, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 6 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 

Clustering(13) Variable = 11P GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   11  2
  11P GAIN WILD-TYPE 45  5
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                 50 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  5 
$`11P GAIN MUTATED`
TCGA-KL-8339 TCGA-KL-8341 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
       28.08        24.79       151.92        23.47        25.91        72.69 
TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       11.21        74.93        80.38        87.78        86.07        77.85 
TCGA-KO-8415 
       57.17 

$`11P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.93        84.89        98.30        96.95        92.55        30.21 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.53        66.54        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.71        62.33         8.12        32.68        13.15        35.57 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
       37.08       123.12        51.02        31.33       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       25.48        65.19         3.52         0.56        52.27        67.82 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       23.41         2.50        36.95        89.65        20.91        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       76.90        10.68        79.04        92.71        16.67       103.27 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             11.21               0.56 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            151.92             137.06 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             72.69              63.12 
[1] "11.2 - 151.9 (72.7)" "0.6 - 137.1 (63.1)" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D13V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         6        4         2        2
  11P GAIN WILD-TYPE      15       19        12        4
D13V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 4                 19
  STAGE III                2                 12
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  11P GAIN MUTATED    6  4     4
  11P GAIN WILD-TYPE 15 19    16
D13V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   6                 15
  T2                   4                 19
  T3+T4                4                 16
                    vv
clus                 N0 N1+N2
  11P GAIN MUTATED   11     2
  11P GAIN WILD-TYPE 29     3
D13V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                2                  3
                    vv
clus                 M0 M1 MX
  11P GAIN MUTATED    7  1  1
  11P GAIN WILD-TYPE 25  1  8
D13V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                7                 25
  M1                1                  1
  MX                1                  8
D13V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5  9
  11P GAIN WILD-TYPE 20 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    9
  11P GAIN WILD-TYPE   20   30
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                5                 20
  MALE                  9                 30
D13V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D13V9, continuous
D13V10, continuous

Clustering(14) Variable = 11Q GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   12  2
  11Q GAIN WILD-TYPE 44  5
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                 49 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  5 
$`11Q GAIN MUTATED`
TCGA-KL-8339 TCGA-KL-8341 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
       28.08        24.79       151.92        23.47        25.91        72.69 
TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
        3.52        11.21        74.93        80.38        87.78        86.07 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`11Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.93        84.89        98.30        96.95        92.55        30.21 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.53        66.54        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.71        62.33         8.12        32.68        13.15        35.57 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
       37.08       123.12        51.02        31.33       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       25.48        65.19         0.56        52.27        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
        2.50        36.95        89.65        20.91        75.72        76.90 
TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 
       10.68        79.04        92.71        16.67       103.27        61.58 
TCGA-KO-8417 
       63.91 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              3.52               0.56 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            151.92             137.06 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             64.93              63.91 
[1] "3.5 - 151.9 (64.9)" "0.6 - 137.1 (63.9)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D14V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         6        4         2        3
  11Q GAIN WILD-TYPE      15       19        12        3
D14V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 4                 19
  STAGE III                2                 12
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  11Q GAIN MUTATED    6  4     5
  11Q GAIN WILD-TYPE 15 19    15
D14V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   6                 15
  T2                   4                 19
  T3+T4                5                 15
                    vv
clus                 N0 N1+N2
  11Q GAIN MUTATED   11     2
  11Q GAIN WILD-TYPE 29     3
D14V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                2                  3
                    vv
clus                 M0 M1 MX
  11Q GAIN MUTATED    7  2  1
  11Q GAIN WILD-TYPE 25  0  8
D14V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                7                 25
  M1                2                  0
  MX                1                  8
D14V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5 10
  11Q GAIN WILD-TYPE 20 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5   10
  11Q GAIN WILD-TYPE   20   29
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                5                 20
  MALE                 10                 29
D14V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D14V9, continuous
D14V10, continuous

Clustering(15) Variable = 12P GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   14  2
  12P GAIN WILD-TYPE 42  5
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                16                 47 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  5 
$`12P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KL-8343 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        28.08        59.67        62.33       151.92        37.08 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.52         0.56        52.27        11.21 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       80.38        87.78        86.07        77.85 

$`12P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 
       86.53        66.54        24.79        73.91        28.80        54.71 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
       31.33       114.18        87.91        25.48        65.19        72.69 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       75.72        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        57.17        61.58        63.91 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.56               2.50 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            151.92             123.12 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             55.97              66.54 
[1] "0.6 - 151.9 (56.0)" "2.5 - 123.1 (66.5)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D15V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         5        7         2        3
  12P GAIN WILD-TYPE      16       16        12        3
D15V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  5                 16
  STAGE II                 7                 16
  STAGE III                2                 12
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  12P GAIN MUTATED    5  7     5
  12P GAIN WILD-TYPE 16 16    15
D15V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                   5                 16
  T2                   7                 16
  T3+T4                5                 15
                    vv
clus                 N0 N1+N2
  12P GAIN MUTATED   13     2
  12P GAIN WILD-TYPE 27     3
D15V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                  13                 27
  N1+N2                2                  3
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED    7  2  2
  12P GAIN WILD-TYPE 25  0  7
D15V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                7                 25
  M1                2                  0
  MX                2                  7
D15V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    5 12
  12P GAIN WILD-TYPE 20 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5   12
  12P GAIN WILD-TYPE   20   27
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                5                 20
  MALE                 12                 27
D15V8, continuous
D15V9, continuous
D15V10, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  6 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KO-8408 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 

Clustering(16) Variable = 12Q GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   13  3
  12Q GAIN WILD-TYPE 43  4
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                 47 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                  4 
$`12Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 TCGA-KM-8438 TCGA-KM-8443 
      137.06        28.08        24.79        59.67       151.92        37.08 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.52         0.56        52.27        11.21 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       80.38        87.78        86.07        77.85 

$`12Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       86.53        66.54        73.91        28.80        54.71        62.33 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
       31.33       114.18        87.91        25.48        65.19        72.69 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       75.72        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        57.17        61.58        63.91 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.56               2.50 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            151.92             123.12 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            44.675             66.540 
[1] "0.6 - 151.9 (44.7)" "2.5 - 123.1 (66.5)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         5        6         2        4
  12Q GAIN WILD-TYPE      16       17        12        2
D16V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  5                 16
  STAGE II                 6                 17
  STAGE III                2                 12
  STAGE IV                 4                  2
                    vv
clus                 T1 T2 T3+T4
  12Q GAIN MUTATED    5  6     6
  12Q GAIN WILD-TYPE 16 17    14
D16V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                   5                 16
  T2                   6                 17
  T3+T4                6                 14
                    vv
clus                 N0 N1+N2
  12Q GAIN MUTATED   12     3
  12Q GAIN WILD-TYPE 28     2
D16V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                  12                 28
  N1+N2                3                  2
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED    7  2  2
  12Q GAIN WILD-TYPE 25  0  7
D16V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                7                 25
  M1                2                  0
  MX                2                  7
D16V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    5 12
  12Q GAIN WILD-TYPE 20 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5   12
  12Q GAIN WILD-TYPE   20   27
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                5                 20
  MALE                 12                 27
D16V8, continuous
D16V9, continuous
D16V10, continuous

Clustering(17) Variable = 14Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   14  2
  14Q GAIN WILD-TYPE 42  5
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                 47 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  5 
$`14Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        98.93        24.79        62.33       151.92        37.08 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91        72.69         3.52        52.27        11.21 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       80.38        87.78        86.07        77.85 

$`14Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       28.08        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 
       31.33       114.18        87.91        25.48        65.19         0.56 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       75.72        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        57.17        61.58        63.91 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.52               0.56 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            151.92             123.12 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             67.51              63.91 
[1] "3.5 - 151.9 (67.5)" "0.6 - 123.1 (63.9)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "14Q GAIN MUTATED"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "14Q GAIN MUTATED"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "14Q GAIN MUTATED"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         6        8         1        2
  14Q GAIN WILD-TYPE      15       15        13        4
D17V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 8                 15
  STAGE III                1                 13
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  14Q GAIN MUTATED    6  8     3
  14Q GAIN WILD-TYPE 15 15    17
D17V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   6                 15
  T2                   8                 15
  T3+T4                3                 17
                    vv
clus                 N0 N1+N2
  14Q GAIN MUTATED   14     1
  14Q GAIN WILD-TYPE 26     4
D17V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  14                 26
  N1+N2                1                  4
                    vv
clus                 M0 M1 MX
  14Q GAIN MUTATED    8  1  2
  14Q GAIN WILD-TYPE 24  1  7
D17V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                8                 24
  M1                1                  1
  MX                2                  7
D17V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    6 11
  14Q GAIN WILD-TYPE 19 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6   11
  14Q GAIN WILD-TYPE   19   28
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                6                 19
  MALE                 11                 28
D17V8, continuous
D17V9, continuous
D17V10, continuous

Clustering(18) Variable = 15Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   14  3
  15Q GAIN WILD-TYPE 42  4
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                17                 46 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                  4 
$`15Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        98.93        30.21        62.33       151.92        37.08 
TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8405 
       23.47        72.69         3.52        52.27        11.21        74.93 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        80.38        86.07        77.85        57.17 

$`15Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 
       98.30        96.95        92.55        44.84        86.53        28.08 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        59.67        28.80        54.71 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       114.18        87.91        25.48        25.91        65.19 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        0.56        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        10.68        79.04        92.71 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       87.78       103.27        61.58        63.91 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3.52               0.56 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            151.92             123.12 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             62.33              64.55 
[1] "3.5 - 151.9 (62.3)" "0.6 - 123.1 (64.5)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED"   "15Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED"   "15Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED"   "15Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED"   "15Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED"   "15Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED"   "15Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         5        8         3        2
  15Q GAIN WILD-TYPE      16       15        11        4
D18V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  5                 16
  STAGE II                 8                 15
  STAGE III                3                 11
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  15Q GAIN MUTATED    5  8     5
  15Q GAIN WILD-TYPE 16 15    15
D18V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   5                 16
  T2                   8                 15
  T3+T4                5                 15
                    vv
clus                 N0 N1+N2
  15Q GAIN MUTATED   14     2
  15Q GAIN WILD-TYPE 26     3
D18V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  14                 26
  N1+N2                2                  3
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED    9  1  2
  15Q GAIN WILD-TYPE 23  1  7
D18V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                9                 23
  M1                1                  1
  MX                2                  7
D18V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7 11
  15Q GAIN WILD-TYPE 18 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7   11
  15Q GAIN WILD-TYPE   18   28
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                7                 18
  MALE                 11                 28
D18V8, continuous
D18V9, continuous
D18V10, continuous

Clustering(19) Variable = 16P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   16  1
  16P GAIN WILD-TYPE 40  6
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                 46 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  6 
$`16P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
      137.06        24.79        62.33       151.92        37.08        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8405 
       25.48        25.91        72.69         3.52        11.21        74.93 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78        86.07        77.85        57.17 

$`16P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        28.08        66.54        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.71         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 
       51.02        31.33       114.18        87.91        65.19         0.56 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        61.58        63.91 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.52               0.56 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            151.92             123.12 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             62.33              64.55 
[1] "3.5 - 151.9 (62.3)" "0.6 - 123.1 (64.5)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         8        6         2        2
  16P GAIN WILD-TYPE      13       17        12        4
D19V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  8                 13
  STAGE II                 6                 17
  STAGE III                2                 12
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  16P GAIN MUTATED    8  6     4
  16P GAIN WILD-TYPE 13 17    16
D19V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                   8                 13
  T2                   6                 17
  T3+T4                4                 16
                    vv
clus                 N0 N1+N2
  16P GAIN MUTATED   15     1
  16P GAIN WILD-TYPE 25     4
D19V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                  15                 25
  N1+N2                1                  4
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED    9  1  2
  16P GAIN WILD-TYPE 23  1  7
D19V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                9                 23
  M1                1                  1
  MX                2                  7
D19V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    7 11
  16P GAIN WILD-TYPE 18 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      7   11
  16P GAIN WILD-TYPE   18   28
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                7                 18
  MALE                 11                 28
D19V8, continuous
D19V9, continuous
D19V10, continuous

Clustering(20) Variable = 16Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   16  1
  16Q GAIN WILD-TYPE 40  6
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                 46 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  6 
$`16Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
      137.06        24.79        62.33       151.92        37.08        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8405 
       25.48        25.91        72.69         3.52        11.21        74.93 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78        86.07        77.85        57.17 

$`16Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        28.08        66.54        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.71         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 
       51.02        31.33       114.18        87.91        65.19         0.56 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        61.58        63.91 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.52               0.56 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            151.92             123.12 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             62.33              64.55 
[1] "3.5 - 151.9 (62.3)" "0.6 - 123.1 (64.5)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         8        6         2        2
  16Q GAIN WILD-TYPE      13       17        12        4
D20V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  8                 13
  STAGE II                 6                 17
  STAGE III                2                 12
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  16Q GAIN MUTATED    8  6     4
  16Q GAIN WILD-TYPE 13 17    16
D20V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                   8                 13
  T2                   6                 17
  T3+T4                4                 16
                    vv
clus                 N0 N1+N2
  16Q GAIN MUTATED   15     1
  16Q GAIN WILD-TYPE 25     4
D20V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                  15                 25
  N1+N2                1                  4
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED    9  1  2
  16Q GAIN WILD-TYPE 23  1  7
D20V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                9                 23
  M1                1                  1
  MX                2                  7
D20V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    7 11
  16Q GAIN WILD-TYPE 18 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      7   11
  16Q GAIN WILD-TYPE   18   28
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                7                 18
  MALE                 11                 28
D20V8, continuous
D20V9, continuous
D20V10, continuous

Clustering(21) Variable = 18P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   12  2
  18P GAIN WILD-TYPE 44  5
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 49 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  5 
$`18P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8422 
      137.06        62.33       151.92        31.33        23.47        25.48 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KO-8404 TCGA-KO-8405 
       25.91        72.69         3.52        52.27        10.68        74.93 
TCGA-KO-8409 TCGA-KO-8410 
       80.38        87.78 

$`18P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.53        28.08        66.54        24.79        73.91        59.67 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.71         8.12        32.68        13.15        35.57 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 
       37.08       123.12        51.02       114.18        87.91        65.19 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        0.56        67.82        23.41         2.50        11.21        36.95 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
       89.65        20.91        75.72        76.90        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       16.67       103.27        86.07        77.85        57.17        61.58 
TCGA-KO-8417 
       63.91 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              3.52               0.56 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            151.92             123.12 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             57.30              65.19 
[1] "3.5 - 151.9 (57.3)" "0.6 - 123.1 (65.2)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         6        5         1        2
  18P GAIN WILD-TYPE      15       18        13        4
D21V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 5                 18
  STAGE III                1                 13
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  18P GAIN MUTATED    6  5     3
  18P GAIN WILD-TYPE 15 18    17
D21V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   6                 15
  T2                   5                 18
  T3+T4                3                 17
                    vv
clus                 N0 N1+N2
  18P GAIN MUTATED   11     0
  18P GAIN WILD-TYPE 29     5
D21V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                0                  5
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED    5  1  2
  18P GAIN WILD-TYPE 27  1  7
D21V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                5                 27
  M1                1                  1
  MX                2                  7
D21V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4 10
  18P GAIN WILD-TYPE 21 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4   10
  18P GAIN WILD-TYPE   21   29
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                 21
  MALE                 10                 29
D21V8, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KO-8411         TCGA-KO-8413 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D21V9, continuous
D21V10, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  6 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KN-8433         TCGA-KO-8408 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 

Clustering(22) Variable = 18Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   12  1
  18Q GAIN WILD-TYPE 44  6
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 50 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                  6 
$`18Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8422 
      137.06        62.33       151.92        31.33        23.47        25.48 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 
       25.91        72.69         3.52        52.27        74.93        80.38 
TCGA-KO-8410 
       87.78 

$`18Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.53        28.08        66.54        24.79        73.91        59.67 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.71         8.12        32.68        13.15        35.57 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 
       37.08       123.12        51.02       114.18        87.91        65.19 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        0.56        67.82        23.41         2.50        11.21        36.95 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
       89.65        20.91        75.72        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67       103.27        86.07        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              3.52               0.56 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            151.92             123.12 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             62.33              64.55 
[1] "3.5 - 151.9 (62.3)" "0.6 - 123.1 (64.5)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         6        5         1        1
  18Q GAIN WILD-TYPE      15       18        13        5
D22V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 5                 18
  STAGE III                1                 13
  STAGE IV                 1                  5
                    vv
clus                 T1 T2 T3+T4
  18Q GAIN MUTATED    6  5     2
  18Q GAIN WILD-TYPE 15 18    18
D22V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   6                 15
  T2                   5                 18
  T3+T4                2                 18
                    vv
clus                 N0 N1+N2
  18Q GAIN MUTATED   11     0
  18Q GAIN WILD-TYPE 29     5
D22V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                0                  5
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    5  1  2
  18Q GAIN WILD-TYPE 27  1  7
D22V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                5                 27
  M1                1                  1
  MX                2                  7
D22V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  9
  18Q GAIN WILD-TYPE 21 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    9
  18Q GAIN WILD-TYPE   21   30
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 21
  MALE                  9                 30
D22V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KO-8411         TCGA-KO-8413 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D22V9, continuous
D22V10, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                  6 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KN-8433         TCGA-KO-8408 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 

Clustering(23) Variable = 19P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   11  5
  19P GAIN WILD-TYPE 45  2
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                16                 47 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                  2 
$`19P GAIN MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
       30.21        28.08        24.79        62.33       151.92        37.08 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       25.91        72.69         3.52         0.56        52.27        11.21 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8414 
       16.67        80.38        87.78        77.85 

$`19P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       98.93        84.89        98.30        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.53        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       31.33       114.18        23.47        87.91        25.48        65.19 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       75.72        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.07        57.17        61.58        63.91 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.56               2.50 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            151.92             137.06 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            33.645             67.820 
[1] "0.6 - 151.9 (33.6)" "2.5 - 137.1 (67.8)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "19P GAIN MUTATED"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "19P GAIN MUTATED"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "19P GAIN MUTATED"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "9.7"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         4        6         2        5
  19P GAIN WILD-TYPE      17       17        12        1
D23V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  4                 17
  STAGE II                 6                 17
  STAGE III                2                 12
  STAGE IV                 5                  1
                    vv
clus                 T1 T2 T3+T4
  19P GAIN MUTATED    4  6     7
  19P GAIN WILD-TYPE 17 17    13
D23V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   4                 17
  T2                   6                 17
  T3+T4                7                 13
                    vv
clus                 N0 N1+N2
  19P GAIN MUTATED   10     5
  19P GAIN WILD-TYPE 30     0
D23V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                  10                 30
  N1+N2                5                  0
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED    6  2  2
  19P GAIN WILD-TYPE 26  0  7
D23V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                6                 26
  M1                2                  0
  MX                2                  7
D23V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    5 12
  19P GAIN WILD-TYPE 20 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5   12
  19P GAIN WILD-TYPE   20   27
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                5                 20
  MALE                 12                 27
D23V8, continuous
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8476         TCGA-KM-8477 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KO-8411         TCGA-KO-8413 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D23V9, continuous
D23V10, continuous

Clustering(24) Variable = 19Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   11  4
  19Q GAIN WILD-TYPE 45  3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                15                 48 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                  3 
$`19Q GAIN MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8423 
       30.21        28.08        62.33       151.92        37.08        25.91 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8408 
       72.69         3.52         0.56        52.27        11.21        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8414 
       80.38        87.78        77.85 

$`19Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       98.93        84.89        98.30        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.71         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.02        31.33       114.18        23.47        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       65.19        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       20.91        75.72        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       92.71       103.27        86.07        57.17        61.58        63.91 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.56               2.50 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            151.92             137.06 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             37.08              67.18 
[1] "0.6 - 151.9 (37.1)" "2.5 - 137.1 (67.2)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "5.4"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         4        6         2        4
  19Q GAIN WILD-TYPE      17       17        12        2
D24V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  4                 17
  STAGE II                 6                 17
  STAGE III                2                 12
  STAGE IV                 4                  2
                    vv
clus                 T1 T2 T3+T4
  19Q GAIN MUTATED    4  6     6
  19Q GAIN WILD-TYPE 17 17    14
D24V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   4                 17
  T2                   6                 17
  T3+T4                6                 14
                    vv
clus                 N0 N1+N2
  19Q GAIN MUTATED   10     4
  19Q GAIN WILD-TYPE 30     1
D24V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                  10                 30
  N1+N2                4                  1
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED    5  2  2
  19Q GAIN WILD-TYPE 27  0  7
D24V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                5                 27
  M1                2                  0
  MX                2                  7
D24V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    5 11
  19Q GAIN WILD-TYPE 20 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5   11
  19Q GAIN WILD-TYPE   20   28
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                5                 20
  MALE                 11                 28
D24V8, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8476         TCGA-KM-8477 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KO-8411         TCGA-KO-8413 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D24V9, continuous
D24V10, continuous

Clustering(25) Variable = 20P GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   14  3
  20P GAIN WILD-TYPE 42  4
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                 46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  4 
$`20P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      137.06        98.93        28.08        24.79        62.33       151.92 
TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       37.08        25.91        72.69         0.56        52.27        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       74.93        80.38        87.78        86.07        77.85 

$`20P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       66.54        73.91        59.67        28.80        54.71         8.12 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       32.68        13.15        35.57       123.12        51.02        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 
      114.18        23.47        87.91        25.48        65.19         3.52 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       75.72        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        57.17        61.58        63.91 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.56               2.50 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            151.92             123.12 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            72.690             62.745 
[1] "0.6 - 151.9 (72.7)" "2.5 - 123.1 (62.7)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         6        7         2        3
  20P GAIN WILD-TYPE      15       16        12        3
D25V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 7                 16
  STAGE III                2                 12
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  20P GAIN MUTATED    6  7     5
  20P GAIN WILD-TYPE 15 16    15
D25V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                   6                 15
  T2                   7                 16
  T3+T4                5                 15
                    vv
clus                 N0 N1+N2
  20P GAIN MUTATED   14     3
  20P GAIN WILD-TYPE 26     2
D25V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                  14                 26
  N1+N2                3                  2
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED    9  1  2
  20P GAIN WILD-TYPE 23  1  7
D25V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                9                 23
  M1                1                  1
  MX                2                  7
D25V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    6 12
  20P GAIN WILD-TYPE 19 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6   12
  20P GAIN WILD-TYPE   19   27
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                6                 19
  MALE                 12                 27
D25V8, continuous
D25V9, continuous
D25V10, continuous

Clustering(26) Variable = 20Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   14  3
  20Q GAIN WILD-TYPE 42  4
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                17                 46 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                  4 
$`20Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      137.06        98.93        28.08        24.79        62.33       151.92 
TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8433 TCGA-KO-8404 
       37.08        25.91        72.69         0.56        11.21        10.68 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       74.93        80.38        87.78        86.07        77.85 

$`20Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       66.54        73.91        59.67        28.80        54.71         8.12 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       32.68        13.15        35.57       123.12        51.02        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 
      114.18        23.47        87.91        25.48        65.19         3.52 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       20.91        75.72        76.90        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        57.17        61.58        63.91 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.56               2.50 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            151.92             123.12 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            72.690             62.745 
[1] "0.6 - 151.9 (72.7)" "2.5 - 123.1 (62.7)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         6        6         2        4
  20Q GAIN WILD-TYPE      15       17        12        2
D26V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  6                 15
  STAGE II                 6                 17
  STAGE III                2                 12
  STAGE IV                 4                  2
                    vv
clus                 T1 T2 T3+T4
  20Q GAIN MUTATED    6  6     6
  20Q GAIN WILD-TYPE 15 17    14
D26V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                   6                 15
  T2                   6                 17
  T3+T4                6                 14
                    vv
clus                 N0 N1+N2
  20Q GAIN MUTATED   13     3
  20Q GAIN WILD-TYPE 27     2
D26V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                  13                 27
  N1+N2                3                  2
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED    9  1  2
  20Q GAIN WILD-TYPE 23  1  7
D26V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                9                 23
  M1                1                  1
  MX                2                  7
D26V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    6 12
  20Q GAIN WILD-TYPE 19 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6   12
  20Q GAIN WILD-TYPE   19   27
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                6                 19
  MALE                 12                 27
D26V8, continuous
D26V9, continuous
D26V10, continuous

Clustering(27) Variable = 21Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    3  0
  21Q GAIN WILD-TYPE 53  7
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 60 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  7 
$`21Q GAIN MUTATED`
TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8433 
      151.92        31.33        11.21 

$`21Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.93        84.89        98.30        96.95        92.55        30.21 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.53        28.08        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 
       59.67        28.80        54.71        62.33         8.12        32.68 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 
       13.15        35.57        37.08       123.12        51.02       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19        72.69 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
        3.52         0.56        52.27        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       36.95        89.65        20.91        75.72        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
       74.93        79.04        92.71        16.67        80.38        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.07        77.85        57.17        61.58        63.91 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             11.21               0.56 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            151.92             137.06 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             31.33              64.55 
[1] "11.2 - 151.9 (31.3)" "0.6 - 137.1 (64.5)" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         1        1         1        0
  21Q GAIN WILD-TYPE      20       22        13        6
D27V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  1                 20
  STAGE II                 1                 22
  STAGE III                1                 13
  STAGE IV                 0                  6
                    vv
clus                 T1 T2 T3+T4
  21Q GAIN MUTATED    1  1     1
  21Q GAIN WILD-TYPE 20 22    19
D27V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                   1                 20
  T2                   1                 22
  T3+T4                1                 19
                    vv
clus                 N0 N1+N2
  21Q GAIN MUTATED    1     0
  21Q GAIN WILD-TYPE 39     5
D27V5, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 44 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8328 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8329         TCGA-KL-8330         TCGA-KL-8331 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8332         TCGA-KL-8333         TCGA-KL-8334 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8336         TCGA-KL-8337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8339         TCGA-KL-8340 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KN-8418         TCGA-KN-8419 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8427 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8429         TCGA-KN-8430 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8413         TCGA-KO-8414         TCGA-KO-8415 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8416         TCGA-KO-8417 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  21Q GAIN MUTATED    0  0  2
  21Q GAIN WILD-TYPE 32  2  7
D27V6, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 41 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8439         TCGA-KM-8440 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8443 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8476         TCGA-KM-8477         TCGA-KN-8426 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8410         TCGA-KO-8411 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8413         TCGA-KO-8414         TCGA-KO-8415 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8416         TCGA-KO-8417 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D27V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 23 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   23   38
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                2                 23
  MALE                  1                 38
D27V8, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KO-8411         TCGA-KO-8413 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D27V9, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  8 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KN-8428         TCGA-KO-8408 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8416 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D27V10, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  6 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KO-8408         TCGA-KO-8409 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 

Clustering(28) Variable = 22Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   13  4
  22Q GAIN WILD-TYPE 43  3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 46 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                  3 
$`22Q GAIN MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8419 
       38.07       137.06        24.79        62.33        37.08        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8405 
       25.91         3.52         0.56        52.27        11.21        74.93 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78        86.07        77.85 

$`22Q GAIN WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.18       102.77        90.48       108.62        98.93        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       28.08        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
      151.92         8.12        32.68        13.15        35.57       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.02        31.33       114.18        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       72.69        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        10.68        79.04        92.71 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        57.17        61.58        63.91 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.56               2.50 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            137.06             151.92 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             38.07              67.18 
[1] "0.6 - 137.1 (38.1)" "2.5 - 151.9 (67.2)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr=" "4.6"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         4        6         4        3
  22Q GAIN WILD-TYPE      17       17        10        3
D28V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  4                 17
  STAGE II                 6                 17
  STAGE III                4                 10
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  22Q GAIN MUTATED    4  6     7
  22Q GAIN WILD-TYPE 17 17    13
D28V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                   4                 17
  T2                   6                 17
  T3+T4                7                 13
                    vv
clus                 N0 N1+N2
  22Q GAIN MUTATED   11     3
  22Q GAIN WILD-TYPE 29     2
D28V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  11                 29
  N1+N2                3                  2
                    vv
clus                 M0 M1 MX
  22Q GAIN MUTATED    9  1  1
  22Q GAIN WILD-TYPE 23  1  8
D28V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                9                 23
  M1                1                  1
  MX                1                  8
D28V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    5 12
  22Q GAIN WILD-TYPE 20 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5   12
  22Q GAIN WILD-TYPE   20   27
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                5                 20
  MALE                 12                 27
D28V8, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                  9 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8476 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D28V9, continuous
D28V10, continuous

Clustering(29) Variable = XQ GAIN MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    9  0
  XQ GAIN WILD-TYPE 47  7
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                54 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 7 
$`XQ GAIN MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KO-8409 
       62.33        23.47        25.91         3.52         0.56        80.38 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       87.78        86.07        77.85 

$`XQ GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.93        84.89        98.30        96.95        92.55        30.21 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.53        28.08        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       59.67        28.80        54.71       151.92         8.12        32.68 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       13.15        35.57        37.08       123.12        51.02        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 
      114.18        87.91        25.48        65.19        72.69        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       67.82        23.41         2.50        11.21        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       20.91        75.72        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67       103.27        57.17        61.58        63.91 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.56              2.50 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            87.78            151.92 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            62.33             64.55 
[1] "0.6 - 87.8 (62.3)"  "2.5 - 151.9 (64.5)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
[1] "hr="   "8e+07"
D29V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         4        4         0        2
  XQ GAIN WILD-TYPE      17       19        14        4
D29V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 4                17
  STAGE II                4                19
  STAGE III               0                14
  STAGE IV                2                 4
                   vv
clus                T1 T2 T3+T4
  XQ GAIN MUTATED    4  4     2
  XQ GAIN WILD-TYPE 17 19    18
D29V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                  4                17
  T2                  4                19
  T3+T4               2                18
                   vv
clus                N0 N1+N2
  XQ GAIN MUTATED    8     1
  XQ GAIN WILD-TYPE 32     4
D29V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                  8                32
  N1+N2               1                 4
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED    5  1  0
  XQ GAIN WILD-TYPE 27  1  9
D29V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               5                27
  M1               1                 1
  MX               0                 9
D29V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  8
  XQ GAIN WILD-TYPE 23 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    8
  XQ GAIN WILD-TYPE   23   31
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               2                23
  MALE                 8                31
D29V8, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                10 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8411 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D29V9, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KO-8416 
"XQ GAIN WILD-TYPE" 
D29V10, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 

Clustering(30) Variable = 1P LOSS MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   42  5
  1P LOSS WILD-TYPE 14  2
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               47                16 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                 2 
$`1P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.93        84.89        98.30        96.95        92.55        30.21 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.53        28.08        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 
       59.67        28.80        54.71       151.92        32.68        35.57 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       37.08       123.12       114.18        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       72.69        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       20.91        76.90        74.93        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        77.85        57.17        61.58        63.91 

$`1P LOSS WILD-TYPE`
TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
       62.33         8.12        13.15        51.02        31.33        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 
       25.91         3.52         0.56        52.27        11.21        75.72 
TCGA-KO-8404 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       10.68        80.38        87.78        86.07 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             2.50              0.56 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           151.92             87.78 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            72.69             28.62 
[1] "2.5 - 151.9 (72.7)" "0.6 - 87.8 (28.6)" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "1P LOSS MUTATED"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
[1] "hr=" "1.9"
D30V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        12       19        13        3
  1P LOSS WILD-TYPE       9        4         1        3
D30V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                12                 9
  STAGE II               19                 4
  STAGE III              13                 1
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  1P LOSS MUTATED   12 19    16
  1P LOSS WILD-TYPE  9  4     4
D30V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                 12                 9
  T2                 19                 4
  T3+T4              16                 4
                   vv
clus                N0 N1+N2
  1P LOSS MUTATED   32     4
  1P LOSS WILD-TYPE  8     1
D30V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                 32                 8
  N1+N2               4                 1
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED   28  1  5
  1P LOSS WILD-TYPE  4  1  4
D30V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              28                 4
  M1               1                 1
  MX               5                 4
D30V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   21 26
  1P LOSS WILD-TYPE  4 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     21   26
  1P LOSS WILD-TYPE    4   13
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              21                 4
  MALE                26                13
D30V8, continuous
D30V9, continuous
D30V10, continuous

Clustering(31) Variable = 1Q LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   41  6
  1Q LOSS WILD-TYPE 15  1
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47                16 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                 1 
$`1Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.53        28.08        66.54        24.79        73.91        59.67 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       28.80        54.71       151.92        32.68        35.57        37.08 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       114.18        87.91        25.48        65.19        72.69 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82        23.41         2.50        36.95        89.65 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       20.91        76.90        74.93        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        77.85        57.17        61.58        63.91 

$`1Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 
      109.18        62.33         8.12        13.15        51.02        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 
       23.47        25.91         3.52         0.56        11.21        75.72 
TCGA-KO-8404 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       10.68        80.38        87.78        86.07 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2.50              0.56 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           151.92            109.18 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            67.82             28.62 
[1] "2.5 - 151.9 (67.8)" "0.6 - 109.2 (28.6)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
[1] "hr=" "1.3"
D31V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        12       20        12        3
  1Q LOSS WILD-TYPE       9        3         2        3
D31V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                12                 9
  STAGE II               20                 3
  STAGE III              12                 2
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  1Q LOSS MUTATED   12 20    15
  1Q LOSS WILD-TYPE  9  3     5
D31V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                 12                 9
  T2                 20                 3
  T3+T4              15                 5
                   vv
clus                N0 N1+N2
  1Q LOSS MUTATED   32     4
  1Q LOSS WILD-TYPE  8     1
D31V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                 32                 8
  N1+N2               4                 1
                   vv
clus                M0 M1 MX
  1Q LOSS MUTATED   27  1  5
  1Q LOSS WILD-TYPE  5  1  4
D31V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0              27                 5
  M1               1                 1
  MX               5                 4
D31V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   21 26
  1Q LOSS WILD-TYPE  4 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     21   26
  1Q LOSS WILD-TYPE    4   13
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              21                 4
  MALE                26                13
D31V8, continuous
D31V9, continuous
D31V10, continuous

Clustering(32) Variable = 2P LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   36  6
  2P LOSS WILD-TYPE 20  1
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               42                21 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6                 1 
$`2P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 
       28.08        66.54        24.79        73.91        54.71       151.92 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8424 
       32.68        35.57        37.08       123.12       114.18        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       72.69        52.27        67.82        23.41         2.50        36.95 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       89.65        20.91        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        77.85        57.17        61.58        63.91 

$`2P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 
      109.18        98.30        59.67        28.80        62.33         8.12 
TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       13.15        51.02        31.33        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.52         0.56        11.21        75.72        10.68 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       80.38        87.78        86.07 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.50              0.56 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           151.92            109.18 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           70.255            31.330 
[1] "2.5 - 151.9 (70.3)" "0.6 - 109.2 (31.3)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "2P LOSS MUTATED"   "2P LOSS MUTATED"   "2P LOSS MUTATED" 
[1] "hr=" "2.1"
D32V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED        11       18        10        3
  2P LOSS WILD-TYPE      10        5         4        3
D32V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                11                10
  STAGE II               18                 5
  STAGE III              10                 4
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  2P LOSS MUTATED   11 18    13
  2P LOSS WILD-TYPE 10  5     7
D32V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1                 11                10
  T2                 18                 5
  T3+T4              13                 7
                   vv
clus                N0 N1+N2
  2P LOSS MUTATED   27     4
  2P LOSS WILD-TYPE 13     1
D32V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                 27                13
  N1+N2               4                 1
                   vv
clus                M0 M1 MX
  2P LOSS MUTATED   24  1  5
  2P LOSS WILD-TYPE  8  1  4
D32V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              24                 8
  M1               1                 1
  MX               5                 4
D32V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   19 23
  2P LOSS WILD-TYPE  6 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     19   23
  2P LOSS WILD-TYPE    6   16
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              19                 6
  MALE                23                16
D32V8, continuous
D32V9, continuous
D32V10, continuous

Clustering(33) Variable = 2Q LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   36  6
  2Q LOSS WILD-TYPE 20  1
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               42                21 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6                 1 
$`2Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 
       28.08        66.54        24.79        73.91        54.71       151.92 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8424 
       32.68        35.57        37.08       123.12       114.18        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       72.69        52.27        67.82        23.41         2.50        36.95 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       89.65        20.91        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        77.85        57.17        61.58        63.91 

$`2Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 
      109.18        98.30        59.67        28.80        62.33         8.12 
TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       13.15        51.02        31.33        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.52         0.56        11.21        75.72        10.68 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       80.38        87.78        86.07 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.50              0.56 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           151.92            109.18 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           70.255            31.330 
[1] "2.5 - 151.9 (70.3)" "0.6 - 109.2 (31.3)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" 
[1] "hr=" "2.1"
D33V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED        11       18        10        3
  2Q LOSS WILD-TYPE      10        5         4        3
D33V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                11                10
  STAGE II               18                 5
  STAGE III              10                 4
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  2Q LOSS MUTATED   11 18    13
  2Q LOSS WILD-TYPE 10  5     7
D33V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1                 11                10
  T2                 18                 5
  T3+T4              13                 7
                   vv
clus                N0 N1+N2
  2Q LOSS MUTATED   27     4
  2Q LOSS WILD-TYPE 13     1
D33V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                 27                13
  N1+N2               4                 1
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED   24  1  5
  2Q LOSS WILD-TYPE  8  1  4
D33V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              24                 8
  M1               1                 1
  MX               5                 4
D33V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   19 23
  2Q LOSS WILD-TYPE  6 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     19   23
  2Q LOSS WILD-TYPE    6   16
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              19                 6
  MALE                23                16
D33V8, continuous
D33V9, continuous
D33V10, continuous

Clustering(34) Variable = 3P LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    7  0
  3P LOSS WILD-TYPE 49  7
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                56 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 7 
$`3P LOSS MUTATED`
TCGA-KL-8333 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8414 
       98.30        87.91        72.69         2.50        20.91        77.85 
TCGA-KO-8415 
       57.17 

$`3P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.93        84.89        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.53        28.08        66.54        24.79        73.91        59.67 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.71        62.33       151.92         8.12        32.68 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       13.15        35.57        37.08       123.12        51.02        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
      114.18        23.47        25.48        25.91        65.19         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
        0.56        52.27        67.82        23.41        11.21        36.95 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       89.65        75.72        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.07 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2.50              0.56 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            98.30            151.92 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            72.69             63.12 
[1] "2.5 - 98.3 (72.7)"  "0.6 - 151.9 (63.1)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr="     "7.9e+07"
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         2        5         0        0
  3P LOSS WILD-TYPE      19       18        14        6
D34V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 2                19
  STAGE II                5                18
  STAGE III               0                14
  STAGE IV                0                 6
                   vv
clus                T1 T2 T3+T4
  3P LOSS MUTATED    2  5     0
  3P LOSS WILD-TYPE 19 18    20
D34V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  2                19
  T2                  5                18
  T3+T4               0                20
                   vv
clus                N0 N1+N2
  3P LOSS MUTATED    5     0
  3P LOSS WILD-TYPE 35     5
D34V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                  5                35
  N1+N2               0                 5
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED    3  0  0
  3P LOSS WILD-TYPE 29  2  9
D34V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               3                29
  M1               0                 2
  MX               0                 9
D34V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    4  3
  3P LOSS WILD-TYPE 21 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    3
  3P LOSS WILD-TYPE   21   36
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               4                21
  MALE                 3                36
D34V8, continuous
D34V9, continuous
D34V10, continuous

Clustering(35) Variable = 3Q LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    6  0
  3Q LOSS WILD-TYPE 50  7
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                57 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 7 
$`3Q LOSS MUTATED`
TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8414 TCGA-KO-8415 
       87.91        72.69         2.50        20.91        77.85        57.17 

$`3Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.93        84.89        98.30        96.95        92.55        30.21 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.53        28.08        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       59.67        28.80        54.71        62.33       151.92         8.12 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       32.68        13.15        35.57        37.08       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       114.18        23.47        25.48        25.91        65.19 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 
        3.52         0.56        52.27        67.82        23.41        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       36.95        89.65        75.72        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 
       86.07        61.58        63.91 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             2.50              0.56 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            87.91            151.92 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            64.93             63.91 
[1] "2.5 - 87.9 (64.9)"  "0.6 - 151.9 (63.9)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr="     "7.6e+07"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         2        4         0        0
  3Q LOSS WILD-TYPE      19       19        14        6
D35V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 2                19
  STAGE II                4                19
  STAGE III               0                14
  STAGE IV                0                 6
                   vv
clus                T1 T2 T3+T4
  3Q LOSS MUTATED    2  4     0
  3Q LOSS WILD-TYPE 19 19    20
D35V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  2                19
  T2                  4                19
  T3+T4               0                20
                   vv
clus                N0 N1+N2
  3Q LOSS MUTATED    4     0
  3Q LOSS WILD-TYPE 36     5
D35V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                  4                36
  N1+N2               0                 5
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    2  0  0
  3Q LOSS WILD-TYPE 30  2  9
D35V6, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                41 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8426 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8405        TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8409 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8416 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8417 
"3Q LOSS WILD-TYPE" 
D35V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    4  2
  3Q LOSS WILD-TYPE 21 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    2
  3Q LOSS WILD-TYPE   21   37
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               4                21
  MALE                 2                37
D35V8, continuous
D35V9, continuous
D35V10, continuous

Clustering(36) Variable = 5P LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    5  1
  5P LOSS WILD-TYPE 51  6
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                57 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 6 
$`5P LOSS MUTATED`
TCGA-KL-8330 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8442 TCGA-KN-8431 TCGA-KO-8405 
      108.62        24.79       151.92        35.57        23.41        74.93 

$`5P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 
       38.07       109.18       137.06       102.77        90.48        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        28.08        66.54        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8443 
       54.71        62.33         8.12        32.68        13.15        37.08 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19        72.69         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82         2.50        11.21        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.07        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.91 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            23.41              0.56 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           151.92            137.06 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            55.25             63.91 
[1] "23.4 - 151.9 (55.2)" "0.6 - 137.1 (63.9)" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D36V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        4         1        1
  5P LOSS WILD-TYPE      21       19        13        5
D36V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                21
  STAGE II                4                19
  STAGE III               1                13
  STAGE IV                1                 5
                   vv
clus                T1 T2 T3+T4
  5P LOSS MUTATED    0  4     2
  5P LOSS WILD-TYPE 21 19    18
D36V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  0                21
  T2                  4                19
  T3+T4               2                18
                   vv
clus                N0 N1+N2
  5P LOSS MUTATED    3     1
  5P LOSS WILD-TYPE 37     4
D36V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                  3                37
  N1+N2               1                 4
                   vv
clus                M0 M1 MX
  5P LOSS MUTATED    3  0  2
  5P LOSS WILD-TYPE 29  2  7
D36V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               3                29
  M1               0                 2
  MX               2                 7
D36V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    3  3
  5P LOSS WILD-TYPE 22 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    3
  5P LOSS WILD-TYPE   22   36
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               3                22
  MALE                 3                36
D36V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8413 
"5P LOSS WILD-TYPE" 
D36V9, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                 8 
       TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D36V10, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                 6 
       TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8433 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 

Clustering(37) Variable = 5Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    5  1
  5Q LOSS WILD-TYPE 51  6
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                57 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 6 
$`5Q LOSS MUTATED`
TCGA-KL-8330 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8442 TCGA-KN-8431 TCGA-KO-8405 
      108.62        24.79       151.92        35.57        23.41        74.93 

$`5Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 
       38.07       109.18       137.06       102.77        90.48        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        28.08        66.54        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8443 
       54.71        62.33         8.12        32.68        13.15        37.08 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19        72.69         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82         2.50        11.21        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       20.91        75.72        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.07        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.91 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            23.41              0.56 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           151.92            137.06 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            55.25             63.91 
[1] "23.4 - 151.9 (55.2)" "0.6 - 137.1 (63.9)" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        4         1        1
  5Q LOSS WILD-TYPE      21       19        13        5
D37V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                21
  STAGE II                4                19
  STAGE III               1                13
  STAGE IV                1                 5
                   vv
clus                T1 T2 T3+T4
  5Q LOSS MUTATED    0  4     2
  5Q LOSS WILD-TYPE 21 19    18
D37V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  0                21
  T2                  4                19
  T3+T4               2                18
                   vv
clus                N0 N1+N2
  5Q LOSS MUTATED    3     1
  5Q LOSS WILD-TYPE 37     4
D37V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                  3                37
  N1+N2               1                 4
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED    3  0  2
  5Q LOSS WILD-TYPE 29  2  7
D37V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               3                29
  M1               0                 2
  MX               2                 7
D37V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    3  3
  5Q LOSS WILD-TYPE 22 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    3
  5Q LOSS WILD-TYPE   22   36
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3                22
  MALE                 3                36
D37V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KO-8411 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8413 
"5Q LOSS WILD-TYPE" 
D37V9, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 8 
       TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D37V10, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 6 
       TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8433 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 

Clustering(38) Variable = 6P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   39  7
  6P LOSS WILD-TYPE 17  0
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               46                17 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                 0 
$`6P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 
       86.53        28.08        66.54        24.79        73.91        54.71 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.92        32.68        35.57        37.08       123.12       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19        72.69        52.27        67.82 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       23.41         2.50        36.95        89.65        20.91        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       10.68        74.93        79.04        92.71        16.67       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.91 

$`6P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.18        59.67        28.80        62.33         8.12        13.15 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.02        31.33        23.47        25.91         3.52         0.56 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       11.21        75.72        80.38        87.78        86.07 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2.50              0.56 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           151.92            109.18 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           70.255            31.330 
[1] "2.5 - 151.9 (70.3)" "0.6 - 109.2 (31.3)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
[1] "hr="     "2.6e+08"
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED        12       20        10        4
  6P LOSS WILD-TYPE       9        3         4        2
D38V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                12                 9
  STAGE II               20                 3
  STAGE III              10                 4
  STAGE IV                4                 2
                   vv
clus                T1 T2 T3+T4
  6P LOSS MUTATED   12 20    14
  6P LOSS WILD-TYPE  9  3     6
D38V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                 12                 9
  T2                 20                 3
  T3+T4              14                 6
                   vv
clus                N0 N1+N2
  6P LOSS MUTATED   30     4
  6P LOSS WILD-TYPE 10     1
D38V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                 30                10
  N1+N2               4                 1
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED   25  1  5
  6P LOSS WILD-TYPE  7  1  4
D38V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              25                 7
  M1               1                 1
  MX               5                 4
D38V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   21 25
  6P LOSS WILD-TYPE  4 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   25
  6P LOSS WILD-TYPE    4   14
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              21                 4
  MALE                25                14
D38V8, continuous
D38V9, continuous
D38V10, continuous

Clustering(39) Variable = 6Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   40  7
  6Q LOSS WILD-TYPE 16  0
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47                16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                 0 
$`6Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 
       86.53        28.08        66.54        24.79        73.91        54.71 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.92        32.68        35.57        37.08       123.12       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
       87.91        25.48        65.19        72.69         0.56        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        77.85        57.17        61.58        63.91 

$`6Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.18        59.67        28.80        62.33         8.12        13.15 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.02        31.33        23.47        25.91         3.52        11.21 
TCGA-KN-8437 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       75.72        80.38        87.78        86.07 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.56              3.52 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           151.92            109.18 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           67.820            41.175 
[1] "0.6 - 151.9 (67.8)" "3.5 - 109.2 (41.2)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
[1] "hr="     "2.6e+08"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        12       20        10        5
  6Q LOSS WILD-TYPE       9        3         4        1
D39V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                12                 9
  STAGE II               20                 3
  STAGE III              10                 4
  STAGE IV                5                 1
                   vv
clus                T1 T2 T3+T4
  6Q LOSS MUTATED   12 20    15
  6Q LOSS WILD-TYPE  9  3     5
D39V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                 12                 9
  T2                 20                 3
  T3+T4              15                 5
                   vv
clus                N0 N1+N2
  6Q LOSS MUTATED   30     5
  6Q LOSS WILD-TYPE 10     0
D39V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                 30                10
  N1+N2               5                 0
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   25  1  5
  6Q LOSS WILD-TYPE  7  1  4
D39V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              25                 7
  M1               1                 1
  MX               5                 4
D39V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   21 26
  6Q LOSS WILD-TYPE  4 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   26
  6Q LOSS WILD-TYPE    4   13
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              21                 4
  MALE                26                13
D39V8, continuous
D39V9, continuous
D39V10, continuous

Clustering(40) Variable = 8P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   10  0
  8P LOSS WILD-TYPE 46  7
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                53 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 7 
$`8P LOSS MUTATED`
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
      137.06        44.84       123.12         2.50        89.65        20.91 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
      103.27        77.85        61.58        63.91 

$`8P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 
       84.89        98.30        96.95        92.55        30.21        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.08        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       35.57        37.08        51.02        31.33       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19        72.69         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
        0.56        52.27        67.82        23.41        11.21        36.95 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       75.72        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       16.67        80.38        87.78        86.07        57.17 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             2.50              0.56 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           137.06            151.92 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            70.88             62.33 
[1] "2.5 - 137.1 (70.9)" "0.6 - 151.9 (62.3)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
[1] "hr="     "2.4e+08"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         4        5         1        0
  8P LOSS WILD-TYPE      17       18        13        6
D40V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 4                17
  STAGE II                5                18
  STAGE III               1                13
  STAGE IV                0                 6
                   vv
clus                T1 T2 T3+T4
  8P LOSS MUTATED    4  5     1
  8P LOSS WILD-TYPE 17 18    19
D40V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  4                17
  T2                  5                18
  T3+T4               1                19
                   vv
clus                N0 N1+N2
  8P LOSS MUTATED    5     0
  8P LOSS WILD-TYPE 35     5
D40V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                  5                35
  N1+N2               0                 5
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED    6  0  1
  8P LOSS WILD-TYPE 26  2  8
D40V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               6                26
  M1               0                 2
  MX               1                 8
D40V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4  6
  8P LOSS WILD-TYPE 21 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    6
  8P LOSS WILD-TYPE   21   33
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               4                21
  MALE                 6                33
D40V8, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8477        TCGA-KM-8639 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8413 
"8P LOSS WILD-TYPE" 
D40V9, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KO-8409 
"8P LOSS WILD-TYPE" 
D40V10, continuous

Clustering(41) Variable = 8Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    9  0
  8Q LOSS WILD-TYPE 47  7
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                54 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                 7 
$`8Q LOSS MUTATED`
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8411 
      137.06        44.84       123.12         2.50        20.91       103.27 
TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       77.85        61.58        63.91 

$`8Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 
       84.89        98.30        96.95        92.55        30.21        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.08        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       35.57        37.08        51.02        31.33       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19        72.69         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
        0.56        52.27        67.82        23.41        11.21        36.95 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       89.65        75.72        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       92.71        16.67        80.38        87.78        86.07        57.17 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             2.50              0.56 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           137.06            151.92 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            63.91             63.76 
[1] "2.5 - 137.1 (63.9)" "0.6 - 151.9 (63.8)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED"   "8Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED"   "8Q LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED"   "8Q LOSS MUTATED" 
[1] "hr="     "8.5e+07"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         4        4         1        0
  8Q LOSS WILD-TYPE      17       19        13        6
D41V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 4                17
  STAGE II                4                19
  STAGE III               1                13
  STAGE IV                0                 6
                   vv
clus                T1 T2 T3+T4
  8Q LOSS MUTATED    4  4     1
  8Q LOSS WILD-TYPE 17 19    19
D41V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  4                17
  T2                  4                19
  T3+T4               1                19
                   vv
clus                N0 N1+N2
  8Q LOSS MUTATED    5     0
  8Q LOSS WILD-TYPE 35     5
D41V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                  5                35
  N1+N2               0                 5
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED    6  0  1
  8Q LOSS WILD-TYPE 26  2  8
D41V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               6                26
  M1               0                 2
  MX               1                 8
D41V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    4  5
  8Q LOSS WILD-TYPE 21 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    5
  8Q LOSS WILD-TYPE   21   34
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               4                21
  MALE                 5                34
D41V8, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                 9 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8477        TCGA-KM-8639 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8413 
"8Q LOSS WILD-TYPE" 
D41V9, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8409 
"8Q LOSS WILD-TYPE" 
D41V10, continuous

Clustering(42) Variable = 9P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    4  2
  9P LOSS WILD-TYPE 52  5
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                57 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 5 
$`9P LOSS MUTATED`
TCGA-KL-8332 TCGA-KL-8343 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8408 TCGA-KO-8415 
       84.89        59.67        20.91        10.68        16.67        57.17 

$`9P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.93        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.53        28.08        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       35.57        37.08       123.12        51.02        31.33       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19        72.69 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
        3.52         0.56        52.27        67.82        23.41         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
       11.21        36.95        89.65        75.72        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       79.04        92.71        80.38        87.78       103.27        86.07 
TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       77.85        61.58        63.91 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            10.68              0.56 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            84.89            151.92 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            39.04             66.54 
[1] "10.7 - 84.9 (39.0)" "0.6 - 151.9 (66.5)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "5"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         2        1         2        1
  9P LOSS WILD-TYPE      19       22        12        5
D42V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 2                19
  STAGE II                1                22
  STAGE III               2                12
  STAGE IV                1                 5
                   vv
clus                T1 T2 T3+T4
  9P LOSS MUTATED    2  1     3
  9P LOSS WILD-TYPE 19 22    17
D42V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  2                19
  T2                  1                22
  T3+T4               3                17
                   vv
clus                N0 N1+N2
  9P LOSS MUTATED    3     1
  9P LOSS WILD-TYPE 37     4
D42V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                  3                37
  N1+N2               1                 4
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED    3  0  0
  9P LOSS WILD-TYPE 29  2  9
D42V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               3                29
  M1               0                 2
  MX               0                 9
D42V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    1  5
  9P LOSS WILD-TYPE 24 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1    5
  9P LOSS WILD-TYPE   24   34
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               1                24
  MALE                 5                34
D42V8, continuous
D42V9, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8409 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KO-8416 
"9P LOSS WILD-TYPE" 
D42V10, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8409 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 

Clustering(43) Variable = 9Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    5  2
  9Q LOSS WILD-TYPE 51  5
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                56 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 5 
$`9Q LOSS MUTATED`
TCGA-KL-8332 TCGA-KL-8343 TCGA-KN-8429 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8408 
       84.89        59.67        67.82        20.91        10.68        16.67 
TCGA-KO-8415 
       57.17 

$`9Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.93        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.53        28.08        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       35.57        37.08       123.12        51.02        31.33       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19        72.69 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.52         0.56        52.27        23.41         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       36.95        89.65        75.72        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        80.38        87.78       103.27        86.07        77.85 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            10.68              0.56 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            84.89            151.92 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           57.170            65.865 
[1] "10.7 - 84.9 (57.2)" "0.6 - 151.9 (65.9)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "3.8"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         2        1         3        1
  9Q LOSS WILD-TYPE      19       22        11        5
D43V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 2                19
  STAGE II                1                22
  STAGE III               3                11
  STAGE IV                1                 5
                   vv
clus                T1 T2 T3+T4
  9Q LOSS MUTATED    2  1     4
  9Q LOSS WILD-TYPE 19 22    16
D43V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  2                19
  T2                  1                22
  T3+T4               4                16
                   vv
clus                N0 N1+N2
  9Q LOSS MUTATED    4     1
  9Q LOSS WILD-TYPE 36     4
D43V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                  4                36
  N1+N2               1                 4
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED    3  0  0
  9Q LOSS WILD-TYPE 29  2  9
D43V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               3                29
  M1               0                 2
  MX               0                 9
D43V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    2  5
  9Q LOSS WILD-TYPE 23 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2    5
  9Q LOSS WILD-TYPE   23   34
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               2                23
  MALE                 5                34
D43V8, continuous
D43V9, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 9 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8409 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KO-8416 
"9Q LOSS WILD-TYPE" 
D43V10, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8409 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 

Clustering(44) Variable = 10P LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   38  7
  10P LOSS WILD-TYPE 18  0
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 18 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                  0 
$`10P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.53        28.08        66.54        24.79        73.91        59.67 
TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
       54.71        32.68        35.57        37.08       123.12       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19        72.69        52.27        67.82 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
        2.50        36.95        89.65        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.91 

$`10P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 
      109.18        28.80        62.33       151.92         8.12        13.15 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.02        31.33        23.47        25.91         3.52         0.56 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
       23.41        11.21        20.91        75.72        87.78        86.07 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              2.50               0.56 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            137.06             151.92 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            72.690             27.355 
[1] "2.5 - 137.1 (72.7)" "0.6 - 151.9 (27.4)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
[1] "hr="     "2.6e+08"
D44V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED        12       18        11        4
  10P LOSS WILD-TYPE       9        5         3        2
D44V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                 12                  9
  STAGE II                18                  5
  STAGE III               11                  3
  STAGE IV                 4                  2
                    vv
clus                 T1 T2 T3+T4
  10P LOSS MUTATED   12 18    15
  10P LOSS WILD-TYPE  9  5     5
D44V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                  12                  9
  T2                  18                  5
  T3+T4               15                  5
                    vv
clus                 N0 N1+N2
  10P LOSS MUTATED   31     4
  10P LOSS WILD-TYPE  9     1
D44V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  31                  9
  N1+N2                4                  1
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED   27  1  4
  10P LOSS WILD-TYPE  5  1  5
D44V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               27                  5
  M1                1                  1
  MX                4                  5
D44V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   19 26
  10P LOSS WILD-TYPE  6 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     19   26
  10P LOSS WILD-TYPE    6   13
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               19                  6
  MALE                 26                 13
D44V8, continuous
D44V9, continuous
[1] "Remove cluster labels:" "10P LOSS WILD-TYPE"    
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" 
      TCGA-KN-8428       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416 
"10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" 
D44V10, continuous
[1] "Remove cluster labels:" "10P LOSS WILD-TYPE"    
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" "10P LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"10P LOSS MUTATED" "10P LOSS MUTATED" 

Clustering(45) Variable = 10Q LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   38  7
  10Q LOSS WILD-TYPE 18  0
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 18 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 7                  0 
$`10Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.53        28.08        66.54        24.79        73.91        59.67 
TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
       54.71        32.68        35.57        37.08       123.12       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19        72.69        52.27        67.82 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
        2.50        36.95        89.65        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.91 

$`10Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 
      109.18        28.80        62.33       151.92         8.12        13.15 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.02        31.33        23.47        25.91         3.52         0.56 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
       23.41        11.21        20.91        75.72        87.78        86.07 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2.50               0.56 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            137.06             151.92 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            72.690             27.355 
[1] "2.5 - 137.1 (72.7)" "0.6 - 151.9 (27.4)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
[1] "hr="     "2.6e+08"
D45V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED        12       18        11        4
  10Q LOSS WILD-TYPE       9        5         3        2
D45V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                 12                  9
  STAGE II                18                  5
  STAGE III               11                  3
  STAGE IV                 4                  2
                    vv
clus                 T1 T2 T3+T4
  10Q LOSS MUTATED   12 18    15
  10Q LOSS WILD-TYPE  9  5     5
D45V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                  12                  9
  T2                  18                  5
  T3+T4               15                  5
                    vv
clus                 N0 N1+N2
  10Q LOSS MUTATED   31     4
  10Q LOSS WILD-TYPE  9     1
D45V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  31                  9
  N1+N2                4                  1
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED   27  1  4
  10Q LOSS WILD-TYPE  5  1  5
D45V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               27                  5
  M1                1                  1
  MX                4                  5
D45V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   19 26
  10Q LOSS WILD-TYPE  6 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     19   26
  10Q LOSS WILD-TYPE    6   13
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               19                  6
  MALE                 26                 13
D45V8, continuous
D45V9, continuous
[1] "Remove cluster labels:" "10Q LOSS WILD-TYPE"    
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" 
      TCGA-KN-8428       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416 
"10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" 
D45V10, continuous
[1] "Remove cluster labels:" "10Q LOSS WILD-TYPE"    
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" "10Q LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"10Q LOSS MUTATED" "10Q LOSS MUTATED" 

Clustering(46) Variable = 11P LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    7  0
  11P LOSS WILD-TYPE 49  7
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 56 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 0                  7 
$`11P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8434 
      102.77        98.93        54.71        37.08         0.56        36.95 
TCGA-KN-8436 
       20.91 

$`11P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       137.06        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.08        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       62.33       151.92         8.12        32.68        13.15        35.57 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19        72.69         3.52        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8437 
       67.82        23.41         2.50        11.21        89.65        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.07        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.56               2.50 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            102.77             151.92 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            37.080             65.865 
[1] "0.6 - 102.8 (37.1)" "2.5 - 151.9 (65.9)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr="     "7.7e+07"
D46V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         0        5         1        1
  11P LOSS WILD-TYPE      21       18        13        5
D46V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 5                 18
  STAGE III                1                 13
  STAGE IV                 1                  5
                    vv
clus                 T1 T2 T3+T4
  11P LOSS MUTATED    0  5     2
  11P LOSS WILD-TYPE 21 18    18
D46V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   0                 21
  T2                   5                 18
  T3+T4                2                 18
                    vv
clus                 N0 N1+N2
  11P LOSS MUTATED    4     1
  11P LOSS WILD-TYPE 36     4
D46V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                   4                 36
  N1+N2                1                  4
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED    3  0  1
  11P LOSS WILD-TYPE 29  2  8
D46V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                3                 29
  M1                0                  2
  MX                1                  8
D46V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    2  5
  11P LOSS WILD-TYPE 23 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2    5
  11P LOSS WILD-TYPE   23   34
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                2                 23
  MALE                  5                 34
D46V8, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 10 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8476 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8413 
"11P LOSS WILD-TYPE" 
D46V9, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  9 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8428         TCGA-KN-8433 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8416 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D46V10, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-KO-8409 
"11P LOSS WILD-TYPE" 

Clustering(47) Variable = 11Q LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    7  0
  11Q LOSS WILD-TYPE 49  7
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 56 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                  7 
$`11Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8434 
      102.77        98.93        54.71        37.08         0.56        36.95 
TCGA-KN-8436 
       20.91 

$`11Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       137.06        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.08        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       62.33       151.92         8.12        32.68        13.15        35.57 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19        72.69         3.52        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8437 
       67.82        23.41         2.50        11.21        89.65        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.07        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.56               2.50 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            102.77             151.92 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            37.080             65.865 
[1] "0.6 - 102.8 (37.1)" "2.5 - 151.9 (65.9)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr="     "7.7e+07"
D47V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         0        5         1        1
  11Q LOSS WILD-TYPE      21       18        13        5
D47V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 5                 18
  STAGE III                1                 13
  STAGE IV                 1                  5
                    vv
clus                 T1 T2 T3+T4
  11Q LOSS MUTATED    0  5     2
  11Q LOSS WILD-TYPE 21 18    18
D47V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   0                 21
  T2                   5                 18
  T3+T4                2                 18
                    vv
clus                 N0 N1+N2
  11Q LOSS MUTATED    4     1
  11Q LOSS WILD-TYPE 36     4
D47V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                   4                 36
  N1+N2                1                  4
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED    3  0  1
  11Q LOSS WILD-TYPE 29  2  8
D47V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                3                 29
  M1                0                  2
  MX                1                  8
D47V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    2  5
  11Q LOSS WILD-TYPE 23 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    5
  11Q LOSS WILD-TYPE   23   34
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                 23
  MALE                  5                 34
D47V8, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8476 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8413 
"11Q LOSS WILD-TYPE" 
D47V9, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8428         TCGA-KN-8433 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8416 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D47V10, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"11Q LOSS WILD-TYPE" 

Clustering(48) Variable = 13Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   33  7
  13Q LOSS WILD-TYPE 23  0
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                 23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                  0 
$`13Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 
       28.08        66.54        24.79       151.92        32.68        35.57 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       114.18        87.91        25.48        65.19        72.69 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.56        52.27        67.82        23.41         2.50        36.95 
TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       89.65        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       16.67        77.85        61.58        63.91 

$`13Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
      109.18        98.30        73.91        59.67        28.80        54.71 
TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       62.33         8.12        13.15        37.08        51.02        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 
       23.47        25.91         3.52        11.21        20.91        75.72 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       80.38        87.78       103.27        86.07        57.17 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.56               3.52 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            151.92             109.18 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            70.255             54.710 
[1] "0.6 - 151.9 (70.3)" "3.5 - 109.2 (54.7)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
[1] "hr="     "3.4e+08"
D48V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED        10       16         9        5
  13Q LOSS WILD-TYPE      11        7         5        1
D48V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 10                 11
  STAGE II                16                  7
  STAGE III                9                  5
  STAGE IV                 5                  1
                    vv
clus                 T1 T2 T3+T4
  13Q LOSS MUTATED   10 16    14
  13Q LOSS WILD-TYPE 11  7     6
D48V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                  10                 11
  T2                  16                  7
  T3+T4               14                  6
                    vv
clus                 N0 N1+N2
  13Q LOSS MUTATED   25     5
  13Q LOSS WILD-TYPE 15     0
D48V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                  25                 15
  N1+N2                5                  0
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   20  1  4
  13Q LOSS WILD-TYPE 12  1  5
D48V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               20                 12
  M1                1                  1
  MX                4                  5
D48V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   19 21
  13Q LOSS WILD-TYPE  6 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     19   21
  13Q LOSS WILD-TYPE    6   18
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               19                  6
  MALE                 21                 18
D48V8, continuous
D48V9, continuous
D48V10, continuous

Clustering(49) Variable = 16P LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  3
  16P LOSS WILD-TYPE 55  4
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 59 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                  4 
$`16P LOSS MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KN-8427 TCGA-KO-8408 
       30.21        28.08         0.56        16.67 

$`16P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       98.93        84.89        98.30        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       35.57        37.08       123.12        51.02        31.33       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19        72.69 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.52        52.27        67.82        23.41         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       36.95        89.65        20.91        75.72        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       74.93        79.04        92.71        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       86.07        77.85        57.17        61.58        63.91 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.56               2.50 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             30.21             151.92 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            22.375             66.540 
[1] "0.6 - 30.2 (22.4)"  "2.5 - 151.9 (66.5)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "37" 
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         0        0         1        3
  16P LOSS WILD-TYPE      21       23        13        3
D49V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 0                 23
  STAGE III                1                 13
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  16P LOSS MUTATED    0  0     4
  16P LOSS WILD-TYPE 21 23    16
D49V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   0                 21
  T2                   0                 23
  T3+T4                4                 16
                    vv
clus                 N0 N1+N2
  16P LOSS MUTATED    0     4
  16P LOSS WILD-TYPE 40     1
D49V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                   0                 40
  N1+N2                4                  1
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED    1  1  0
  16P LOSS WILD-TYPE 31  1  9
D49V6, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 41 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8340         TCGA-KL-8341 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8342         TCGA-KL-8343         TCGA-KL-8344 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KL-8346         TCGA-KM-8438 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KN-8426 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8410         TCGA-KO-8411 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8413         TCGA-KO-8414         TCGA-KO-8415 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8416         TCGA-KO-8417 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D49V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  3
  16P LOSS WILD-TYPE 24 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    3
  16P LOSS WILD-TYPE   24   36
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 24
  MALE                  3                 36
D49V8, continuous
D49V9, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                  9 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8409         TCGA-KO-8416 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D49V10, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8409 
"16P LOSS WILD-TYPE" 

Clustering(50) Variable = 16Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    1  4
  16Q LOSS WILD-TYPE 55  3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 58 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                  3 
$`16Q LOSS MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8408 
       30.21        28.08         0.56        52.27        16.67 

$`16Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       98.93        84.89        98.30        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.53        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.71        62.33       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       35.57        37.08       123.12        51.02        31.33       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19        72.69 
TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        3.52        67.82        23.41         2.50        11.21        36.95 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       89.65        20.91        75.72        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       79.04        92.71        80.38        87.78       103.27        86.07 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.91 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.56               2.50 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             52.27             151.92 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             28.08              67.18 
[1] "0.6 - 52.3 (28.1)"  "2.5 - 151.9 (67.2)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "28" 
D50V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         0        1         1        3
  16Q LOSS WILD-TYPE      21       22        13        3
D50V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 1                 22
  STAGE III                1                 13
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  16Q LOSS MUTATED    0  1     4
  16Q LOSS WILD-TYPE 21 22    16
D50V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   0                 21
  T2                   1                 22
  T3+T4                4                 16
                    vv
clus                 N0 N1+N2
  16Q LOSS MUTATED    1     4
  16Q LOSS WILD-TYPE 39     1
D50V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                   1                 39
  N1+N2                4                  1
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED    1  1  0
  16Q LOSS WILD-TYPE 31  1  9
D50V6, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 41 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8337 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8340         TCGA-KL-8341 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8342         TCGA-KL-8343         TCGA-KL-8344 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KL-8346         TCGA-KM-8438 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KN-8426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8410         TCGA-KO-8411 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8413         TCGA-KO-8414         TCGA-KO-8415 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8416         TCGA-KO-8417 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D50V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  4
  16Q LOSS WILD-TYPE 24 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    4
  16Q LOSS WILD-TYPE   24   35
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                1                 24
  MALE                  4                 35
D50V8, continuous
D50V9, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                  8 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8416 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D50V10, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"16Q LOSS WILD-TYPE" 

Clustering(51) Variable = 17P LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   40  6
  17P LOSS WILD-TYPE 16  1
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                 17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 6                  1 
$`17P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KL-8346 
       28.08        66.54        24.79        73.91        54.71        62.33 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.92        32.68        35.57        37.08       123.12       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19        72.69        52.27        67.82 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       23.41         2.50        36.95        89.65        20.91        76.90 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.91 

$`17P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 
      109.18        98.30        59.67        28.80         8.12        13.15 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.02        31.33        23.47        25.91         3.52         0.56 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 
       11.21        75.72        10.68        87.78        86.07 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              2.50               0.56 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            151.92             109.18 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            70.255             28.800 
[1] "2.5 - 151.9 (70.3)" "0.6 - 109.2 (28.8)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
[1] "hr=" "1.4"
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED        12       21        10        3
  17P LOSS WILD-TYPE       9        2         4        3
D51V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 12                  9
  STAGE II                21                  2
  STAGE III               10                  4
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  17P LOSS MUTATED   12 21    13
  17P LOSS WILD-TYPE  9  2     7
D51V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                  12                  9
  T2                  21                  2
  T3+T4               13                  7
                    vv
clus                 N0 N1+N2
  17P LOSS MUTATED   31     4
  17P LOSS WILD-TYPE  9     1
D51V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                  31                  9
  N1+N2                4                  1
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   26  1  5
  17P LOSS WILD-TYPE  6  1  4
D51V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               26                  6
  M1                1                  1
  MX                5                  4
D51V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   21 25
  17P LOSS WILD-TYPE  4 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     21   25
  17P LOSS WILD-TYPE    4   14
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               21                  4
  MALE                 25                 14
D51V8, continuous
D51V9, continuous
[1] "Remove cluster labels:" "17P LOSS WILD-TYPE"    
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-KN-8428       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
D51V10, continuous
[1] "Remove cluster labels:" "17P LOSS WILD-TYPE"    
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"17P LOSS MUTATED" "17P LOSS MUTATED" 

Clustering(52) Variable = 17Q LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   40  6
  17Q LOSS WILD-TYPE 16  1
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                 17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                  1 
$`17Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       137.06       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KL-8346 
       28.08        66.54        24.79        73.91        54.71        62.33 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.92        32.68        35.57        37.08       123.12       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19        72.69        52.27        67.82 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       23.41         2.50        36.95        89.65        20.91        76.90 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.91 

$`17Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 
      109.18        98.30        59.67        28.80         8.12        13.15 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.02        31.33        23.47        25.91         3.52         0.56 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 
       11.21        75.72        10.68        87.78        86.07 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2.50               0.56 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            151.92             109.18 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            70.255             28.800 
[1] "2.5 - 151.9 (70.3)" "0.6 - 109.2 (28.8)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
[1] "hr=" "1.4"
D52V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED        12       21        10        3
  17Q LOSS WILD-TYPE       9        2         4        3
D52V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                 12                  9
  STAGE II                21                  2
  STAGE III               10                  4
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  17Q LOSS MUTATED   12 21    13
  17Q LOSS WILD-TYPE  9  2     7
D52V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                  12                  9
  T2                  21                  2
  T3+T4               13                  7
                    vv
clus                 N0 N1+N2
  17Q LOSS MUTATED   31     4
  17Q LOSS WILD-TYPE  9     1
D52V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                  31                  9
  N1+N2                4                  1
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED   26  1  5
  17Q LOSS WILD-TYPE  6  1  4
D52V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               26                  6
  M1                1                  1
  MX                5                  4
D52V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   21 25
  17Q LOSS WILD-TYPE  4 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21   25
  17Q LOSS WILD-TYPE    4   14
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               21                  4
  MALE                 25                 14
D52V8, continuous
D52V9, continuous
[1] "Remove cluster labels:" "17Q LOSS WILD-TYPE"    
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" 
      TCGA-KN-8428       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" 
D52V10, continuous
[1] "Remove cluster labels:" "17Q LOSS WILD-TYPE"    
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                  2 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" "17Q LOSS MUTATED" 
      TCGA-KO-8408       TCGA-KO-8409 
"17Q LOSS MUTATED" "17Q LOSS MUTATED" 

Clustering(53) Variable = 18P LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    5  1
  18P LOSS WILD-TYPE 51  6
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 57 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  6 
$`18P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 TCGA-KN-8427 TCGA-KN-8429 
      102.77        90.48        98.93        30.21         0.56        67.82 

$`18P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 
       38.07       109.18       137.06       108.62        84.89        98.30 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       96.95        92.55        44.84        86.53        28.08        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        59.67        28.80        54.71        62.33 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.92         8.12        32.68        13.15        35.57        37.08 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19        72.69         3.52        52.27 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       23.41         2.50        11.21        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       75.72        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.07        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       57.17        61.58        63.91 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.56               2.50 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            102.77             151.92 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             79.15              62.33 
[1] "0.6 - 102.8 (79.2)" "2.5 - 151.9 (62.3)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D53V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         1        2         1        2
  18P LOSS WILD-TYPE      20       21        13        4
D53V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  1                 20
  STAGE II                 2                 21
  STAGE III                1                 13
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  18P LOSS MUTATED    1  2     3
  18P LOSS WILD-TYPE 20 21    17
D53V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                   1                 20
  T2                   2                 21
  T3+T4                3                 17
                    vv
clus                 N0 N1+N2
  18P LOSS MUTATED    4     2
  18P LOSS WILD-TYPE 36     3
D53V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                   4                 36
  N1+N2                2                  3
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED    4  0  0
  18P LOSS WILD-TYPE 28  2  9
D53V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                4                 28
  M1                0                  2
  MX                0                  9
D53V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  2
  18P LOSS WILD-TYPE 21 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    2
  18P LOSS WILD-TYPE   21   37
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                4                 21
  MALE                  2                 37
D53V8, continuous
D53V9, continuous
D53V10, continuous

Clustering(54) Variable = 18Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    6  2
  18Q LOSS WILD-TYPE 50  5
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 55 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  5 
$`18Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 TCGA-KN-8424 TCGA-KN-8427 
      102.77        90.48        98.93        30.21        65.19         0.56 
TCGA-KN-8429 TCGA-KO-8404 
       67.82        10.68 

$`18Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 
       38.07       109.18       137.06       108.62        84.89        98.30 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       96.95        92.55        44.84        86.53        28.08        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        59.67        28.80        54.71        62.33 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.92         8.12        32.68        13.15        35.57        37.08 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8431 
       25.48        25.91        72.69         3.52        52.27        23.41 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        36.95        89.65        20.91        75.72 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       76.90        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.07        77.85        57.17        61.58 
TCGA-KO-8417 
       63.91 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.56               2.50 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            102.77             151.92 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            66.505             62.330 
[1] "0.6 - 102.8 (66.5)" "2.5 - 151.9 (62.3)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         2        2         1        3
  18Q LOSS WILD-TYPE      19       21        13        3
D54V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  2                 19
  STAGE II                 2                 21
  STAGE III                1                 13
  STAGE IV                 3                  3
                    vv
clus                 T1 T2 T3+T4
  18Q LOSS MUTATED    2  2     4
  18Q LOSS WILD-TYPE 19 21    16
D54V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                   2                 19
  T2                   2                 21
  T3+T4                4                 16
                    vv
clus                 N0 N1+N2
  18Q LOSS MUTATED    5     2
  18Q LOSS WILD-TYPE 35     3
D54V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                   5                 35
  N1+N2                2                  3
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED    4  0  0
  18Q LOSS WILD-TYPE 28  2  9
D54V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                4                 28
  M1                0                  2
  MX                0                  9
D54V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    5  3
  18Q LOSS WILD-TYPE 20 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    3
  18Q LOSS WILD-TYPE   20   36
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                5                 20
  MALE                  3                 36
D54V8, continuous
D54V9, continuous
D54V10, continuous

Clustering(55) Variable = 20P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3  1
  20P LOSS WILD-TYPE 53  6
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 59 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  6 
$`20P LOSS MUTATED`
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KN-8434 
       92.55        30.21        86.53        36.95 

$`20P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8337 TCGA-KL-8339 
       98.93        84.89        98.30        96.95        44.84        28.08 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        59.67        28.80        54.71 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       62.33       151.92         8.12        32.68        13.15        35.57 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       37.08       123.12        51.02        31.33       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19        72.69         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.56        52.27        67.82        23.41         2.50        11.21 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       89.65        20.91        75.72        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       86.07        77.85        57.17        61.58        63.91 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             30.21               0.56 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             92.55             151.92 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             61.74              63.91 
[1] "30.2 - 92.5 (61.7)" "0.6 - 151.9 (63.9)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0        1         2        1
  20P LOSS WILD-TYPE      21       22        12        5
D55V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 1                 22
  STAGE III                2                 12
  STAGE IV                 1                  5
                    vv
clus                 T1 T2 T3+T4
  20P LOSS MUTATED    0  1     3
  20P LOSS WILD-TYPE 21 22    17
D55V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                   0                 21
  T2                   1                 22
  T3+T4                3                 17
                    vv
clus                 N0 N1+N2
  20P LOSS MUTATED    2     1
  20P LOSS WILD-TYPE 38     4
D55V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                   2                 38
  N1+N2                1                  4
                    vv
clus                 M0 M1 MX
  20P LOSS MUTATED    3  0  0
  20P LOSS WILD-TYPE 29  2  9
D55V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                3                 29
  M1                0                  2
  MX                0                  9
D55V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    2  2
  20P LOSS WILD-TYPE 23 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    2
  20P LOSS WILD-TYPE   23   37
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 23
  MALE                  2                 37
D55V8, continuous
D55V9, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  9 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8428         TCGA-KN-8433 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8416 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D55V10, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8409 
"20P LOSS WILD-TYPE" 

Clustering(56) Variable = 20Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    2  1
  20Q LOSS WILD-TYPE 54  6
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 60 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                  6 
$`20Q LOSS MUTATED`
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 
       92.55        30.21        86.53 

$`20Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8337 TCGA-KL-8339 
       98.93        84.89        98.30        96.95        44.84        28.08 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        59.67        28.80        54.71 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       62.33       151.92         8.12        32.68        13.15        35.57 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       37.08       123.12        51.02        31.33       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19        72.69         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.56        52.27        67.82        23.41         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       36.95        89.65        20.91        75.72        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
       74.93        79.04        92.71        16.67        80.38        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.07        77.85        57.17        61.58        63.91 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             30.21               0.56 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             92.55             151.92 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             86.53              63.12 
[1] "30.2 - 92.5 (86.5)" "0.6 - 151.9 (63.1)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED"   "20Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED"   "20Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED"   "20Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"20Q LOSS WILD-TYPE"   "20Q LOSS MUTATED" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        0         2        1
  20Q LOSS WILD-TYPE      21       23        12        5
D56V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                 21
  STAGE II                 0                 23
  STAGE III                2                 12
  STAGE IV                 1                  5
                    vv
clus                 T1 T2 T3+T4
  20Q LOSS MUTATED    0  0     3
  20Q LOSS WILD-TYPE 21 23    17
D56V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                   0                 21
  T2                   0                 23
  T3+T4                3                 17
                    vv
clus                 N0 N1+N2
  20Q LOSS MUTATED    2     1
  20Q LOSS WILD-TYPE 38     4
D56V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                   2                 38
  N1+N2                1                  4
                    vv
clus                 M0 M1 MX
  20Q LOSS MUTATED    3  0  0
  20Q LOSS WILD-TYPE 29  2  9
D56V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                3                 29
  M1                0                  2
  MX                0                  9
D56V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 24 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   24   37
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 24
  MALE                  2                 37
D56V8, continuous
D56V9, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8428         TCGA-KN-8433 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8416 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D56V10, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"20Q LOSS WILD-TYPE" 

Clustering(57) Variable = 21Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   26  6
  21Q LOSS WILD-TYPE 30  1
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                 31 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                  1 
$`21Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 
       38.07       102.77       108.62        98.93        84.89        96.95 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8343 
       30.21        86.53        28.08        66.54        24.79        59.67 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8422 TCGA-KN-8424 
       28.80        62.33        37.08       123.12        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 
       72.69         0.56        52.27        67.82         2.50        36.95 
TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       76.90        79.04        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 
       57.17        61.58 

$`21Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8337 
      109.18       137.06        90.48        98.30        92.55        44.84 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       73.91        54.71       151.92         8.12        32.68        13.15 
TCGA-KM-8442 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
       35.57        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 
       25.91         3.52        23.41        11.21        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8413 
       75.72        10.68        74.93        92.71        87.78        86.07 
TCGA-KO-8417 
       63.91 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.56               3.52 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            123.12             151.92 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             63.76              63.91 
[1] "0.6 - 123.1 (63.8)" "3.5 - 151.9 (63.9)"
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
[1] "hr=" "5.1"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         9       11         8        4
  21Q LOSS WILD-TYPE      12       12         6        2
D57V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  9                 12
  STAGE II                11                 12
  STAGE III                8                  6
  STAGE IV                 4                  2
                    vv
clus                 T1 T2 T3+T4
  21Q LOSS MUTATED    9 11    12
  21Q LOSS WILD-TYPE 12 12     8
D57V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                   9                 12
  T2                  11                 12
  T3+T4               12                  8
                    vv
clus                 N0 N1+N2
  21Q LOSS MUTATED   21     5
  21Q LOSS WILD-TYPE 19     0
D57V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                  21                 19
  N1+N2                5                  0
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   19  1  2
  21Q LOSS WILD-TYPE 13  1  7
D57V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               19                 13
  M1                1                  1
  MX                2                  7
D57V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   13 19
  21Q LOSS WILD-TYPE 12 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     13   19
  21Q LOSS WILD-TYPE   12   20
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               13                 12
  MALE                 19                 20
D57V8, continuous
D57V9, continuous
D57V10, continuous

Clustering(58) Variable = 22Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    6  2
  22Q LOSS WILD-TYPE 50  5
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 55 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                  5 
$`22Q LOSS MUTATED`
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8422 
      108.62        98.93        30.21        28.08       151.92        25.48 
TCGA-KN-8436 TCGA-KO-8415 
       20.91        57.17 

$`22Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8332 
       38.07       109.18       137.06       102.77        90.48        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       98.30        96.95        92.55        44.84        86.53        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        59.67        28.80        54.71        62.33 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
        8.12        32.68        13.15        35.57        37.08       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8423 
       51.02        31.33       114.18        23.47        87.91        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19        72.69         3.52         0.56        52.27        67.82 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       23.41         2.50        11.21        36.95        89.65        75.72 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
       80.38        87.78       103.27        86.07        77.85        61.58 
TCGA-KO-8417 
       63.91 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             20.91               0.56 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            151.92             137.06 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             43.69              65.19 
[1] "20.9 - 151.9 (43.7)" "0.6 - 137.1 (65.2)" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8323         TCGA-KL-8326         TCGA-KL-8327 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8329         TCGA-KL-8330 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8339 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8439 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8440         TCGA-KM-8441         TCGA-KM-8442 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8443         TCGA-KM-8476         TCGA-KM-8477 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8418         TCGA-KN-8419 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8431         TCGA-KN-8432         TCGA-KN-8433 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         2        4         0        2
  22Q LOSS WILD-TYPE      19       19        14        4
D58V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  2                 19
  STAGE II                 4                 19
  STAGE III                0                 14
  STAGE IV                 2                  4
                    vv
clus                 T1 T2 T3+T4
  22Q LOSS MUTATED    2  4     2
  22Q LOSS WILD-TYPE 19 19    18
D58V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                   2                 19
  T2                   4                 19
  T3+T4                2                 18
                    vv
clus                 N0 N1+N2
  22Q LOSS MUTATED    5     2
  22Q LOSS WILD-TYPE 35     3
D58V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                   5                 35
  N1+N2                2                  3
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED    4  1  1
  22Q LOSS WILD-TYPE 28  1  8
D58V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                4                 28
  M1                1                  1
  MX                1                  8
D58V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    6  2
  22Q LOSS WILD-TYPE 19 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6    2
  22Q LOSS WILD-TYPE   19   37
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                6                 19
  MALE                  2                 37
D58V8, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 10 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8413 
"22Q LOSS WILD-TYPE" 
D58V9, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-KL-8335         TCGA-KL-8341         TCGA-KL-8345 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8428         TCGA-KN-8433 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8416 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D58V10, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-KL-8335         TCGA-KL-8341         TCGA-KL-8345 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-KO-8409 
"22Q LOSS WILD-TYPE" 

Clustering(59) Variable = XQ LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   34  6
  XQ LOSS WILD-TYPE 22  1
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               40                23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                 1 
$`XQ LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
       38.07       102.77        90.48       108.62        98.93        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.30        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KM-8440 
       28.08        66.54        73.91        59.67        54.71        32.68 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       35.57       123.12       114.18        87.91        25.48        65.19 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 
       52.27        67.82        23.41         2.50        11.21        89.65 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       20.91        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        57.17        61.58        63.91 

$`XQ LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 
      109.18       137.06        24.79        28.80        62.33       151.92 
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
        8.12        13.15        37.08        51.02        31.33        23.47 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8434 TCGA-KN-8437 
       25.91        72.69         3.52         0.56        36.95        75.72 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       74.93        80.38        87.78        86.07        77.85 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2.50              0.56 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           123.12            151.92 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           65.865            51.020 
[1] "2.5 - 123.1 (65.9)" "0.6 - 151.9 (51.0)"
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8323        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8337        TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KL-8341        TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8439 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8440        TCGA-KM-8441        TCGA-KM-8442        TCGA-KM-8443 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8418 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8426        TCGA-KN-8427 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8428        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KN-8433        TCGA-KN-8434        TCGA-KN-8435        TCGA-KN-8436 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-KN-8437        TCGA-KO-8403        TCGA-KO-8404        TCGA-KO-8405 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8410        TCGA-KO-8411        TCGA-KO-8413        TCGA-KO-8414 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
[1] "hr=" "2.9"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED        10       16        11        3
  XQ LOSS WILD-TYPE      11        7         3        3
D59V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                10                11
  STAGE II               16                 7
  STAGE III              11                 3
  STAGE IV                3                 3
                   vv
clus                T1 T2 T3+T4
  XQ LOSS MUTATED   10 16    14
  XQ LOSS WILD-TYPE 11  7     6
D59V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                 10                11
  T2                 16                 7
  T3+T4              14                 6
                   vv
clus                N0 N1+N2
  XQ LOSS MUTATED   25     3
  XQ LOSS WILD-TYPE 15     2
D59V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 25                15
  N1+N2               3                 2
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED   22  1  3
  XQ LOSS WILD-TYPE 10  1  6
D59V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              22                10
  M1               1                 1
  MX               3                 6
D59V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   18 22
  XQ LOSS WILD-TYPE  7 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     18   22
  XQ LOSS WILD-TYPE    7   17
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              18                 7
  MALE                22                17
D59V8, continuous
D59V9, continuous
D59V10, continuous
> q(save="no")
