
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/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/KICH-TP/3472422/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/3351134/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] "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" ""  

nPatients in clinical file=25, in cluster file=66, common to both=25
[1] "Reduce the number of clustering variables from 80 to 43."
[1] 43 25
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3                22 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3                22 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3                22 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3                22 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
               10                15 
      4P GAIN CNV 4P GAIN WILD-TYPE 
               10                15 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                9                16 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                9                16 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
                9                16 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                9                16 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                9                16 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                9                16 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
                8                17 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                8                17 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                9                16 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                9                16 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4                21 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4                21 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                4                21 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                4                21 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 8                 17 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 8                 17 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 9                 16 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 9                 16 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 7                 18 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 7                 18 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 6                 19 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 6                 19 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 9                 16 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 9                 16 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 8                 17 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 8                 17 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 8                 17 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 8                 17 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 8                 17 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 8                 17 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 8                 17 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 8                 17 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 8                 17 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 8                 17 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                 19 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                 19 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 5                 20 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 5                 20 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 7                 18 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 7                 18 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 7                 18 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 7                 18 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 7                 18 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 7                 18 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                5                20 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                5                20 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               14                11 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               14                11 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               14                11 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               14                11 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
               13                12 
      2P LOSS CNV 2P LOSS WILD-TYPE 
               13                12 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
               13                12 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
               13                12 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4                21 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4                21 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                4                21 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                4                21 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               15                10 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               15                10 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               15                10 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               15                10 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3                22 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3                22 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                12                 13 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                12                 13 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                12                 13 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                12                 13 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                13                 12 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                13                 12 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                15                 10 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                15                 10 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                15                 10 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                15                 10 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 3                 22 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 3                 22 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 9                 16 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 9                 16 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                9                16 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                9                16 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[11] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[13] "YEAROFTOBACCOSMOKINGONSET"        "DISTANT.METASTASIS"              
[15] "LYMPH.NODE.METASTASIS"            "TUMOR.STAGECODE"                 
[17] "NEOPLASM.DISEASESTAGE"            "BATCHNUMBER"                     

Input Data has 18 rows and 25 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
        3126           NA         4335          247         1552         3473 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
         714         2674          775          788         1983         2211 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8430 TCGA-KN-8431 
         107           17           NA         2063           NA          712 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
          76          341         1124         2727          636         2303 
TCGA-KO-8409 
        2445 
Variable 1:'AGE':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NUMBERPACKYEARSSMOKED':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "GENDER"                "DISTANT.METASTASIS"   
[4] "LYMPH.NODE.METASTASIS" "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE"
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T1A T1B  T2 T2B T3A  T4 
  3   5   8   4   4   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 25 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=24, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 3p gain
D1V1, survival
                   sevent
clus2                0  1
  3P GAIN CNV        1  1
  3P GAIN WILD-TYPE 21  1
      3P GAIN CNV 3P GAIN WILD-TYPE 
                2                22 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                 1 
$`3P GAIN CNV`
TCGA-KN-8427 TCGA-KN-8428 
        0.56        52.27 

$`3P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        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-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-8409 
       89.65        20.91        75.72        80.38 

      3P GAIN CNV 3P GAIN WILD-TYPE 
             0.56              2.50 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            52.27            142.52 
      3P GAIN CNV 3P GAIN WILD-TYPE 
           26.415            43.985 
[1] "0.6 - 52.3 (26.4)"  "2.5 - 142.5 (44.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3P GAIN WILD-TYPE"       "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3P GAIN WILD-TYPE"       "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3P GAIN WILD-TYPE"       "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                2                22 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3P GAIN WILD-TYPE" "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-8409 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          0    3
  3P GAIN WILD-TYPE   11   11
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  FEMALE           0                11
  MALE             3                11
                   vv
clus                M0 M1 MX
  3P GAIN CNV        0  0  0
  3P GAIN WILD-TYPE  2  2  3
D1V4, multiclass
                   vv
clus                N0 N1 NX
  3P GAIN CNV        2  1  0
  3P GAIN WILD-TYPE 11  1 10
D1V5, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  N0           2                11
  N1           1                 1
  NX           0                10
D1V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN CNV             1        1         0        1
  3P GAIN WILD-TYPE       7       11         2        2
D1V7, multiclass
           clus
vv          3P GAIN CNV 3P GAIN WILD-TYPE
  STAGE I             1                 7
  STAGE II            1                11
  STAGE III           0                 2
  STAGE IV            1                 2

Clustering(2) Variable = 3q gain
D2V1, survival
                   sevent
clus2                0  1
  3Q GAIN CNV        1  1
  3Q GAIN WILD-TYPE 21  1
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                2                22 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                 1 
$`3Q GAIN CNV`
TCGA-KN-8427 TCGA-KN-8428 
        0.56        52.27 

$`3Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        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-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-8409 
       89.65        20.91        75.72        80.38 

      3Q GAIN CNV 3Q GAIN WILD-TYPE 
             0.56              2.50 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            52.27            142.52 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
           26.415            43.985 
[1] "0.6 - 52.3 (26.4)"  "2.5 - 142.5 (44.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                2                22 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8429        TCGA-KN-8431        TCGA-KN-8432 
"3Q GAIN WILD-TYPE" "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-8409 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          0    3
  3Q GAIN WILD-TYPE   11   11
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  FEMALE           0                11
  MALE             3                11
                   vv
clus                M0 M1 MX
  3Q GAIN CNV        0  0  0
  3Q GAIN WILD-TYPE  2  2  3
D2V4, multiclass
                   vv
clus                N0 N1 NX
  3Q GAIN CNV        2  1  0
  3Q GAIN WILD-TYPE 11  1 10
D2V5, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  N0           2                11
  N1           1                 1
  NX           0                10
D2V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN CNV             1        1         0        1
  3Q GAIN WILD-TYPE       7       11         2        2
D2V7, multiclass
           clus
vv          3Q GAIN CNV 3Q GAIN WILD-TYPE
  STAGE I             1                 7
  STAGE II            1                11
  STAGE III           0                 2
  STAGE IV            1                 2

Clustering(3) Variable = 4p gain
D3V1, survival
                   sevent
clus2                0  1
  4P GAIN CNV        8  1
  4P GAIN WILD-TYPE 14  1
      4P GAIN CNV 4P GAIN WILD-TYPE 
                9                15 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                 1 
$`4P GAIN CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
       28.08       142.52        23.47        25.48        25.91        72.69 
TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8409 
        3.52        11.21        80.38 

$`4P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 
      102.77         8.12        51.02       114.18        87.91        65.19 
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-KN-8436 TCGA-KN-8437 
       89.65        20.91        75.72 

      4P GAIN CNV 4P GAIN WILD-TYPE 
             3.52              0.56 
      4P GAIN CNV 4P GAIN WILD-TYPE 
           142.52            114.18 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            25.91             52.27 
[1] "3.5 - 142.5 (25.9)" "0.6 - 114.2 (52.3)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"4P GAIN WILD-TYPE"       "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"4P GAIN WILD-TYPE"       "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"4P GAIN WILD-TYPE"       "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
[1] "hr=" "2.6"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          3    7
  4P GAIN WILD-TYPE    8    7
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  FEMALE           3                 8
  MALE             7                 7
                   vv
clus                M0 M1 MX
  4P GAIN CNV        1  2  1
  4P GAIN WILD-TYPE  1  0  2
D3V4, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  M0           1                 1
  M1           2                 0
  MX           1                 2
                   vv
clus                N0 N1 NX
  4P GAIN CNV        7  1  2
  4P GAIN WILD-TYPE  6  1  8
D3V5, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  N0           7                 6
  N1           1                 1
  NX           2                 8
D3V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN CNV             4        3         1        2
  4P GAIN WILD-TYPE       4        9         1        1
D3V7, multiclass
           clus
vv          4P GAIN CNV 4P GAIN WILD-TYPE
  STAGE I             4                 4
  STAGE II            3                 9
  STAGE III           1                 1
  STAGE IV            2                 1

Clustering(4) Variable = 4q gain
D4V1, survival
                   sevent
clus2                0  1
  4Q GAIN CNV        8  1
  4Q GAIN WILD-TYPE 14  1
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                9                15 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                 1 
$`4Q GAIN CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
       28.08       142.52        23.47        25.48        25.91        72.69 
TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8409 
        3.52        11.21        80.38 

$`4Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 
      102.77         8.12        51.02       114.18        87.91        65.19 
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-KN-8436 TCGA-KN-8437 
       89.65        20.91        75.72 

      4Q GAIN CNV 4Q GAIN WILD-TYPE 
             3.52              0.56 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
           142.52            114.18 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
            25.91             52.27 
[1] "3.5 - 142.5 (25.9)" "0.6 - 114.2 (52.3)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"4Q GAIN WILD-TYPE"       "4Q GAIN CNV"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "4Q GAIN CNV"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "4Q GAIN CNV" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"4Q GAIN WILD-TYPE"       "4Q GAIN CNV"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "4Q GAIN CNV"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "4Q GAIN CNV" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"4Q GAIN WILD-TYPE"       "4Q GAIN CNV"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "4Q GAIN CNV"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "4Q GAIN CNV" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" 
[1] "hr=" "2.6"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN CNV          3    6
  4Q GAIN WILD-TYPE    8    8
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  FEMALE           3                 8
  MALE             6                 8
                   vv
clus                M0 M1 MX
  4Q GAIN CNV        1  2  1
  4Q GAIN WILD-TYPE  1  0  2
D4V4, multiclass
    clus
vv   4Q GAIN CNV 4Q GAIN WILD-TYPE
  M0           1                 1
  M1           2                 0
  MX           1                 2
                   vv
clus                N0 N1 NX
  4Q GAIN CNV        6  1  2
  4Q GAIN WILD-TYPE  7  1  8
D4V5, multiclass
    clus
vv   4Q GAIN CNV 4Q GAIN WILD-TYPE
  N0           6                 7
  N1           1                 1
  NX           2                 8
D4V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN CNV             3        3         1        2
  4Q GAIN WILD-TYPE       5        9         1        1
D4V7, multiclass
           clus
vv          4Q GAIN CNV 4Q GAIN WILD-TYPE
  STAGE I             3                 5
  STAGE II            3                 9
  STAGE III           1                 1
  STAGE IV            2                 1

Clustering(5) Variable = 7p gain
D5V1, survival
                   sevent
clus2                0  1
  7P GAIN CNV        7  1
  7P GAIN WILD-TYPE 15  1
      7P GAIN CNV 7P GAIN WILD-TYPE 
                8                16 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                1                 1 
$`7P GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
      142.52        23.47        25.91        72.69         3.52        52.27 
TCGA-KN-8433 TCGA-KO-8409 
       11.21        80.38 

$`7P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19         0.56        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       36.95        89.65        20.91        75.72 

      7P GAIN CNV 7P GAIN WILD-TYPE 
             3.52              0.56 
      7P GAIN CNV 7P GAIN WILD-TYPE 
           142.52            114.18 
      7P GAIN CNV 7P GAIN WILD-TYPE 
           39.090            43.985 
[1] "3.5 - 142.5 (39.1)" "0.6 - 114.2 (44.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
[1] "hr=" "2.1"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          2    7
  7P GAIN WILD-TYPE    9    7
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  FEMALE           2                 9
  MALE             7                 7
                   vv
clus                M0 M1 MX
  7P GAIN CNV        1  1  1
  7P GAIN WILD-TYPE  1  1  2
D5V4, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  7P GAIN CNV        7  0  2
  7P GAIN WILD-TYPE  6  2  8
D5V5, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  N0           7                 6
  N1           0                 2
  NX           2                 8
D5V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN CNV             3        4         1        1
  7P GAIN WILD-TYPE       5        8         1        2
D5V7, multiclass
           clus
vv          7P GAIN CNV 7P GAIN WILD-TYPE
  STAGE I             3                 5
  STAGE II            4                 8
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(6) Variable = 7q gain
D6V1, survival
                   sevent
clus2                0  1
  7Q GAIN CNV        7  1
  7Q GAIN WILD-TYPE 15  1
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                8                16 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                1                 1 
$`7Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
      142.52        23.47        25.91        72.69         3.52        52.27 
TCGA-KN-8433 TCGA-KO-8409 
       11.21        80.38 

$`7Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19         0.56        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       36.95        89.65        20.91        75.72 

      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             3.52              0.56 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
           142.52            114.18 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
           39.090            43.985 
[1] "3.5 - 142.5 (39.1)" "0.6 - 114.2 (44.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
[1] "hr=" "2.1"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          2    7
  7Q GAIN WILD-TYPE    9    7
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  FEMALE           2                 9
  MALE             7                 7
                   vv
clus                M0 M1 MX
  7Q GAIN CNV        1  1  1
  7Q GAIN WILD-TYPE  1  1  2
D6V4, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  7Q GAIN CNV        7  0  2
  7Q GAIN WILD-TYPE  6  2  8
D6V5, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  N0           7                 6
  N1           0                 2
  NX           2                 8
D6V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN CNV             3        4         1        1
  7Q GAIN WILD-TYPE       5        8         1        2
D6V7, multiclass
           clus
vv          7Q GAIN CNV 7Q GAIN WILD-TYPE
  STAGE I             3                 5
  STAGE II            4                 8
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(7) Variable = 8p gain
D7V1, survival
                   sevent
clus2                0  1
  8P GAIN CNV        5  2
  8P GAIN WILD-TYPE 17  0
      8P GAIN CNV 8P GAIN WILD-TYPE 
                7                17 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                2                 0 
$`8P GAIN CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8427 TCGA-KN-8428 
       28.08       142.52        23.47        25.91         0.56        52.27 
TCGA-KO-8409 
       80.38 

$`8P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77         8.12        51.02       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19        72.69         3.52        67.82        23.41         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       11.21        36.95        89.65        20.91        75.72 

      8P GAIN CNV 8P GAIN WILD-TYPE 
             0.56              2.50 
      8P GAIN CNV 8P GAIN WILD-TYPE 
           142.52            114.18 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            28.08             51.02 
[1] "0.6 - 142.5 (28.1)" "2.5 - 114.2 (51.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
[1] "hr="     "7.2e+09"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          1    7
  8P GAIN WILD-TYPE   10    7
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  FEMALE           1                10
  MALE             7                 7
                   vv
clus                M0 M1 MX
  8P GAIN CNV        1  1  1
  8P GAIN WILD-TYPE  1  1  2
D7V4, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  8P GAIN CNV        6  2  0
  8P GAIN WILD-TYPE  7  0 10
D7V5, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  N0           6                 7
  N1           2                 0
  NX           0                10
D7V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN CNV             2        4         0        2
  8P GAIN WILD-TYPE       6        8         2        1
D7V7, multiclass
           clus
vv          8P GAIN CNV 8P GAIN WILD-TYPE
  STAGE I             2                 6
  STAGE II            4                 8
  STAGE III           0                 2
  STAGE IV            2                 1

Clustering(8) Variable = 8q gain
D8V1, survival
                   sevent
clus2                0  1
  8Q GAIN CNV        6  2
  8Q GAIN WILD-TYPE 16  0
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                8                16 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                2                 0 
$`8Q GAIN CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       28.08       142.52        23.47        25.91         3.52         0.56 
TCGA-KN-8428 TCGA-KO-8409 
       52.27        80.38 

$`8Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77         8.12        51.02       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19        72.69        67.82        23.41         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       36.95        89.65        20.91        75.72 

      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             0.56              2.50 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
           142.52            114.18 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
           26.995            58.105 
[1] "0.6 - 142.5 (27.0)" "2.5 - 114.2 (58.1)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
[1] "hr="     "7.2e+09"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          1    8
  8Q GAIN WILD-TYPE   10    6
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  FEMALE           1                10
  MALE             8                 6
                   vv
clus                M0 M1 MX
  8Q GAIN CNV        1  2  1
  8Q GAIN WILD-TYPE  1  0  2
D8V4, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  M0           1                 1
  M1           2                 0
  MX           1                 2
                   vv
clus                N0 N1 NX
  8Q GAIN CNV        6  2  1
  8Q GAIN WILD-TYPE  7  0  9
D8V5, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  N0           6                 7
  N1           2                 0
  NX           1                 9
D8V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN CNV             2        4         0        3
  8Q GAIN WILD-TYPE       6        8         2        0
D8V7, multiclass
           clus
vv          8Q GAIN CNV 8Q GAIN WILD-TYPE
  STAGE I             2                 6
  STAGE II            4                 8
  STAGE III           0                 2
  STAGE IV            3                 0

Clustering(9) Variable = 9p gain
D9V1, survival
                   sevent
clus2                0  1
  9P GAIN CNV        3  1
  9P GAIN WILD-TYPE 19  1
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4                20 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                1                 1 
$`9P GAIN CNV`
TCGA-KM-8438 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8409 
      142.52         0.56        52.27        80.38 

$`9P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
      102.77        28.08         8.12        51.02       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-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 
       20.91        75.72 

      9P GAIN CNV 9P GAIN WILD-TYPE 
             0.56              2.50 
      9P GAIN CNV 9P GAIN WILD-TYPE 
           142.52            114.18 
      9P GAIN CNV 9P GAIN WILD-TYPE 
           66.325            32.515 
[1] "0.6 - 142.5 (66.3)" "2.5 - 114.2 (32.5)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
[1] "hr=" "3.1"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          1    3
  9P GAIN WILD-TYPE   10   11
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  FEMALE           1                10
  MALE             3                11
                   vv
clus                M0 M1 MX
  9P GAIN CNV        1  0  1
  9P GAIN WILD-TYPE  1  2  2
D9V4, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2                 5 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8439        TCGA-KM-8477 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8426 
"9P GAIN WILD-TYPE" 
                   vv
clus                N0 N1 NX
  9P GAIN CNV        3  1  0
  9P GAIN WILD-TYPE 10  1 10
D9V5, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  N0           3                10
  N1           1                 1
  NX           0                10
D9V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN CNV             0        3         0        1
  9P GAIN WILD-TYPE       8        9         2        2
D9V7, multiclass
           clus
vv          9P GAIN CNV 9P GAIN WILD-TYPE
  STAGE I             0                 8
  STAGE II            3                 9
  STAGE III           0                 2
  STAGE IV            1                 2

Clustering(10) Variable = 9q gain
D10V1, survival
                   sevent
clus2                0  1
  9Q GAIN CNV        3  1
  9Q GAIN WILD-TYPE 19  1
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                4                20 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                1                 1 
$`9Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8409 
      142.52         0.56        52.27        80.38 

$`9Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
      102.77        28.08         8.12        51.02       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-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 
       20.91        75.72 

      9Q GAIN CNV 9Q GAIN WILD-TYPE 
             0.56              2.50 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
           142.52            114.18 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
           66.325            32.515 
[1] "0.6 - 142.5 (66.3)" "2.5 - 114.2 (32.5)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
[1] "hr=" "3.1"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          1    3
  9Q GAIN WILD-TYPE   10   11
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  FEMALE           1                10
  MALE             3                11
                   vv
clus                M0 M1 MX
  9Q GAIN CNV        1  0  1
  9Q GAIN WILD-TYPE  1  2  2
D10V4, multiclass
[1] "Remove cluster labels:" "9Q GAIN CNV"           
clus
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                2                 5 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8439        TCGA-KM-8477 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8426 
"9Q GAIN WILD-TYPE" 
                   vv
clus                N0 N1 NX
  9Q GAIN CNV        3  1  0
  9Q GAIN WILD-TYPE 10  1 10
D10V5, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  N0           3                10
  N1           1                 1
  NX           0                10
D10V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN CNV             0        3         0        1
  9Q GAIN WILD-TYPE       8        9         2        2
D10V7, multiclass
           clus
vv          9Q GAIN CNV 9Q GAIN WILD-TYPE
  STAGE I             0                 8
  STAGE II            3                 9
  STAGE III           0                 2
  STAGE IV            1                 2

Clustering(11) Variable = 11p gain
D11V1, survival
                    sevent
clus2                 0  1
  11P GAIN CNV        6  1
  11P GAIN WILD-TYPE 16  1
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 7                 17 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                  1 
$`11P GAIN CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8433 
       28.08       142.52        23.47        25.91        72.69        11.21 
TCGA-KO-8409 
       80.38 

$`11P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77         8.12        51.02       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19         3.52         0.56        52.27        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        36.95        89.65        20.91        75.72 

      11P GAIN CNV 11P GAIN WILD-TYPE 
             11.21               0.56 
      11P GAIN CNV 11P GAIN WILD-TYPE 
            142.52             114.18 
      11P GAIN CNV 11P GAIN WILD-TYPE 
             28.08              51.02 
[1] "11.2 - 142.5 (28.1)" "0.6 - 114.2 (51.0)" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"11P GAIN WILD-TYPE"       "11P GAIN CNV"       "11P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "11P GAIN CNV" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"11P GAIN WILD-TYPE"       "11P GAIN CNV"       "11P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "11P GAIN CNV" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"11P GAIN WILD-TYPE"       "11P GAIN CNV"       "11P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "11P GAIN CNV" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
[1] "hr=" "2.6"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN CNV          2    6
  11P GAIN WILD-TYPE    9    8
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  11P GAIN CNV        1  1  1
  11P GAIN WILD-TYPE  1  1  2
D11V4, multiclass
    clus
vv   11P GAIN CNV 11P GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  11P GAIN CNV        6  1  1
  11P GAIN WILD-TYPE  7  1  9
D11V5, multiclass
    clus
vv   11P GAIN CNV 11P GAIN WILD-TYPE
  N0            6                  7
  N1            1                  1
  NX            1                  9
D11V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN CNV             3        3         1        1
  11P GAIN WILD-TYPE       5        9         1        2
D11V7, multiclass
           clus
vv          11P GAIN CNV 11P GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             3                  9
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(12) Variable = 11q gain
D12V1, survival
                    sevent
clus2                 0  1
  11Q GAIN CNV        7  1
  11Q GAIN WILD-TYPE 15  1
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 8                 16 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                  1 
$`11Q GAIN CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       28.08       142.52        23.47        25.91        72.69         3.52 
TCGA-KN-8433 TCGA-KO-8409 
       11.21        80.38 

$`11Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77         8.12        51.02       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19         0.56        52.27        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       36.95        89.65        20.91        75.72 

      11Q GAIN CNV 11Q GAIN WILD-TYPE 
              3.52               0.56 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
            142.52             114.18 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
            26.995             51.645 
[1] "3.5 - 142.5 (27.0)" "0.6 - 114.2 (51.6)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV"       "11Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV"       "11Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV"       "11Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
[1] "hr=" "2.6"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          2    7
  11Q GAIN WILD-TYPE    9    7
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              7                  7
                    vv
clus                 M0 M1 MX
  11Q GAIN CNV        1  2  1
  11Q GAIN WILD-TYPE  1  0  2
D12V4, multiclass
    clus
vv   11Q GAIN CNV 11Q GAIN WILD-TYPE
  M0            1                  1
  M1            2                  0
  MX            1                  2
                    vv
clus                 N0 N1 NX
  11Q GAIN CNV        6  1  2
  11Q GAIN WILD-TYPE  7  1  8
D12V5, multiclass
    clus
vv   11Q GAIN CNV 11Q GAIN WILD-TYPE
  N0            6                  7
  N1            1                  1
  NX            2                  8
D12V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN CNV             3        3         1        2
  11Q GAIN WILD-TYPE       5        9         1        1
D12V7, multiclass
           clus
vv          11Q GAIN CNV 11Q GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             3                  9
  STAGE III            1                  1
  STAGE IV             2                  1

Clustering(13) Variable = 12p gain
D13V1, survival
                    sevent
clus2                 0  1
  12P GAIN CNV        5  1
  12P GAIN WILD-TYPE 17  1
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 6                 18 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 1                  1 
$`12P GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8428 TCGA-KO-8409 
      142.52        23.47        25.91         3.52        52.27        80.38 

$`12P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 
       25.48        65.19        72.69         0.56        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 

      12P GAIN CNV 12P GAIN WILD-TYPE 
              3.52               0.56 
      12P GAIN CNV 12P GAIN WILD-TYPE 
            142.52             114.18 
      12P GAIN CNV 12P GAIN WILD-TYPE 
            39.090             43.985 
[1] "3.5 - 142.5 (39.1)" "0.6 - 114.2 (44.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
[1] "hr=" "3.1"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          1    6
  12P GAIN WILD-TYPE   10    8
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  FEMALE            1                 10
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  12P GAIN CNV        1  1  1
  12P GAIN WILD-TYPE  1  1  2
D13V4, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  12P GAIN CNV        6  0  1
  12P GAIN WILD-TYPE  7  2  9
D13V5, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  N0            6                  7
  N1            0                  2
  NX            1                  9
D13V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN CNV             2        4         0        1
  12P GAIN WILD-TYPE       6        8         2        2
D13V7, multiclass
           clus
vv          12P GAIN CNV 12P GAIN WILD-TYPE
  STAGE I              2                  6
  STAGE II             4                  8
  STAGE III            0                  2
  STAGE IV             1                  2

Clustering(14) Variable = 12q gain
D14V1, survival
                    sevent
clus2                 0  1
  12Q GAIN CNV        5  0
  12Q GAIN WILD-TYPE 17  2
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 5                 19 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 0                  2 
$`12Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KO-8409 
      142.52        23.47        25.91         3.52        80.38 

$`12Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       25.48        65.19        72.69         0.56        52.27        67.82 
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 
       75.72 

      12Q GAIN CNV 12Q GAIN WILD-TYPE 
              3.52               0.56 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
            142.52             114.18 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
             25.91              51.02 
[1] "3.5 - 142.5 (25.9)" "0.6 - 114.2 (51.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
[1] "hr="     "2.4e+08"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          1    5
  12Q GAIN WILD-TYPE   10    9
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  FEMALE            1                 10
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  12Q GAIN CNV        1  1  1
  12Q GAIN WILD-TYPE  1  1  2
D14V4, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  12Q GAIN CNV        5  0  1
  12Q GAIN WILD-TYPE  8  2  9
D14V5, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  N0            5                  8
  N1            0                  2
  NX            1                  9
D14V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN CNV             2        3         0        1
  12Q GAIN WILD-TYPE       6        9         2        2
D14V7, multiclass
           clus
vv          12Q GAIN CNV 12Q GAIN WILD-TYPE
  STAGE I              2                  6
  STAGE II             3                  9
  STAGE III            0                  2
  STAGE IV             1                  2

Clustering(15) Variable = 14q gain
D15V1, survival
                    sevent
clus2                 0  1
  14Q GAIN CNV        7  1
  14Q GAIN WILD-TYPE 15  1
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 8                 16 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                  1 
$`14Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
      142.52        23.47        25.91        72.69         3.52        52.27 
TCGA-KN-8433 TCGA-KO-8409 
       11.21        80.38 

$`14Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19         0.56        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       36.95        89.65        20.91        75.72 

      14Q GAIN CNV 14Q GAIN WILD-TYPE 
              3.52               0.56 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
            142.52             114.18 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
            39.090             43.985 
[1] "3.5 - 142.5 (39.1)" "0.6 - 114.2 (44.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
[1] "hr=" "2.1"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          2    7
  14Q GAIN WILD-TYPE    9    7
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              7                  7
                    vv
clus                 M0 M1 MX
  14Q GAIN CNV        1  1  1
  14Q GAIN WILD-TYPE  1  1  2
D15V4, multiclass
    clus
vv   14Q GAIN CNV 14Q GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  14Q GAIN CNV        7  0  2
  14Q GAIN WILD-TYPE  6  2  8
D15V5, multiclass
    clus
vv   14Q GAIN CNV 14Q GAIN WILD-TYPE
  N0            7                  6
  N1            0                  2
  NX            2                  8
D15V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN CNV             3        4         1        1
  14Q GAIN WILD-TYPE       5        8         1        2
D15V7, multiclass
           clus
vv          14Q GAIN CNV 14Q GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             4                  8
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(16) Variable = 15q gain
D16V1, survival
                    sevent
clus2                 0  1
  15Q GAIN CNV        6  1
  15Q GAIN WILD-TYPE 16  1
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 7                 17 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                  1 
$`15Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 
      142.52        23.47        72.69         3.52        52.27        11.21 
TCGA-KO-8409 
       80.38 

$`15Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 
       25.48        25.91        65.19         0.56        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        36.95        89.65        20.91        75.72 

      15Q GAIN CNV 15Q GAIN WILD-TYPE 
              3.52               0.56 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
            142.52             114.18 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
             52.27              36.95 
[1] "3.5 - 142.5 (52.3)" "0.6 - 114.2 (37.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
[1] "hr=" "2.1"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          2    6
  15Q GAIN WILD-TYPE    9    8
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  15Q GAIN CNV        1  1  1
  15Q GAIN WILD-TYPE  1  1  2
D16V4, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  15Q GAIN CNV        6  0  2
  15Q GAIN WILD-TYPE  7  2  8
D16V5, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  N0            6                  7
  N1            0                  2
  NX            2                  8
D16V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN CNV             2        4         1        1
  15Q GAIN WILD-TYPE       6        8         1        2
D16V7, multiclass
           clus
vv          15Q GAIN CNV 15Q GAIN WILD-TYPE
  STAGE I              2                  6
  STAGE II             4                  8
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(17) Variable = 16p gain
D17V1, survival
                    sevent
clus2                 0  1
  16P GAIN CNV        7  0
  16P GAIN WILD-TYPE 15  2
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 7                 17 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 0                  2 
$`16P GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
      142.52        23.47        25.48        25.91         3.52        11.21 
TCGA-KO-8409 
       80.38 

$`16P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19        72.69         0.56        52.27        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        36.95        89.65        20.91        75.72 

      16P GAIN CNV 16P GAIN WILD-TYPE 
              3.52               0.56 
      16P GAIN CNV 16P GAIN WILD-TYPE 
            142.52             114.18 
      16P GAIN CNV 16P GAIN WILD-TYPE 
             25.48              52.27 
[1] "3.5 - 142.5 (25.5)" "0.6 - 114.2 (52.3)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
[1] "hr="     "2.4e+08"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          3    5
  16P GAIN WILD-TYPE    8    9
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  FEMALE            3                  8
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  16P GAIN CNV        1  1  1
  16P GAIN WILD-TYPE  1  1  2
D17V4, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  16P GAIN CNV        6  0  2
  16P GAIN WILD-TYPE  7  2  8
D17V5, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  N0            6                  7
  N1            0                  2
  NX            2                  8
D17V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN CNV             3        3         1        1
  16P GAIN WILD-TYPE       5        9         1        2
D17V7, multiclass
           clus
vv          16P GAIN CNV 16P GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             3                  9
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(18) Variable = 16q gain
D18V1, survival
                    sevent
clus2                 0  1
  16Q GAIN CNV        7  0
  16Q GAIN WILD-TYPE 15  2
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 7                 17 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 0                  2 
$`16Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
      142.52        23.47        25.48        25.91         3.52        11.21 
TCGA-KO-8409 
       80.38 

$`16Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19        72.69         0.56        52.27        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        36.95        89.65        20.91        75.72 

      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              3.52               0.56 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
            142.52             114.18 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
             25.48              52.27 
[1] "3.5 - 142.5 (25.5)" "0.6 - 114.2 (52.3)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
[1] "hr="     "2.4e+08"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          3    5
  16Q GAIN WILD-TYPE    8    9
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  FEMALE            3                  8
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  16Q GAIN CNV        1  1  1
  16Q GAIN WILD-TYPE  1  1  2
D18V4, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  16Q GAIN CNV        6  0  2
  16Q GAIN WILD-TYPE  7  2  8
D18V5, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  N0            6                  7
  N1            0                  2
  NX            2                  8
D18V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN CNV             3        3         1        1
  16Q GAIN WILD-TYPE       5        9         1        2
D18V7, multiclass
           clus
vv          16Q GAIN CNV 16Q GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             3                  9
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(19) Variable = 18p gain
D19V1, survival
                    sevent
clus2                 0  1
  18P GAIN CNV        7  1
  18P GAIN WILD-TYPE 15  1
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 8                 16 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                  1 
$`18P GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      142.52        23.47        25.48        25.91        72.69         3.52 
TCGA-KN-8428 TCGA-KO-8409 
       52.27        80.38 

$`18P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19         0.56        67.82        23.41         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       36.95        89.65        20.91        75.72 

      18P GAIN CNV 18P GAIN WILD-TYPE 
              3.52               0.56 
      18P GAIN CNV 18P GAIN WILD-TYPE 
            142.52             114.18 
      18P GAIN CNV 18P GAIN WILD-TYPE 
            39.090             43.985 
[1] "3.5 - 142.5 (39.1)" "0.6 - 114.2 (44.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
[1] "hr=" "2.1"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          2    6
  18P GAIN WILD-TYPE    9    8
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  18P GAIN CNV        1  1  1
  18P GAIN WILD-TYPE  1  1  2
D19V4, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  18P GAIN CNV        7  0  1
  18P GAIN WILD-TYPE  6  2  9
D19V5, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  N0            7                  6
  N1            0                  2
  NX            1                  9
D19V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN CNV             3        4         0        1
  18P GAIN WILD-TYPE       5        8         2        2
D19V7, multiclass
           clus
vv          18P GAIN CNV 18P GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             4                  8
  STAGE III            0                  2
  STAGE IV             1                  2

Clustering(20) Variable = 18q gain
D20V1, survival
                    sevent
clus2                 0  1
  18Q GAIN CNV        7  1
  18Q GAIN WILD-TYPE 15  1
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 8                 16 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                  1 
$`18Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      142.52        23.47        25.48        25.91        72.69         3.52 
TCGA-KN-8428 TCGA-KO-8409 
       52.27        80.38 

$`18Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
      102.77        28.08         8.12        51.02       114.18        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19         0.56        67.82        23.41         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       36.95        89.65        20.91        75.72 

      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              3.52               0.56 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
            142.52             114.18 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
            39.090             43.985 
[1] "3.5 - 142.5 (39.1)" "0.6 - 114.2 (44.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
[1] "hr=" "2.1"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          2    6
  18Q GAIN WILD-TYPE    9    8
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  18Q GAIN CNV        1  1  1
  18Q GAIN WILD-TYPE  1  1  2
D20V4, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  18Q GAIN CNV        7  0  1
  18Q GAIN WILD-TYPE  6  2  9
D20V5, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  N0            7                  6
  N1            0                  2
  NX            1                  9
D20V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN CNV             3        4         0        1
  18Q GAIN WILD-TYPE       5        8         2        2
D20V7, multiclass
           clus
vv          18Q GAIN CNV 18Q GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             4                  8
  STAGE III            0                  2
  STAGE IV             1                  2

Clustering(21) Variable = 19p gain
D21V1, survival
                    sevent
clus2                 0  1
  19P GAIN CNV        5  0
  19P GAIN WILD-TYPE 17  2
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 5                 19 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 0                  2 
$`19P GAIN CNV`
TCGA-KM-8438 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8409 
      142.52        25.91         3.52        11.21        80.38 

$`19P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
      102.77        28.08         8.12        51.02       114.18        23.47 
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-KN-8437 
       75.72 

      19P GAIN CNV 19P GAIN WILD-TYPE 
              3.52               0.56 
      19P GAIN CNV 19P GAIN WILD-TYPE 
            142.52             114.18 
      19P GAIN CNV 19P GAIN WILD-TYPE 
             25.91              51.02 
[1] "3.5 - 142.5 (25.9)" "0.6 - 114.2 (51.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
[1] "hr="     "2.4e+08"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          2    4
  19P GAIN WILD-TYPE    9   10
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              4                 10
                    vv
clus                 M0 M1 MX
  19P GAIN CNV        1  1  1
  19P GAIN WILD-TYPE  1  1  2
D21V4, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  19P GAIN CNV        4  0  2
  19P GAIN WILD-TYPE  9  2  8
D21V5, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  N0            4                  9
  N1            0                  2
  NX            2                  8
D21V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN CNV             2        2         1        1
  19P GAIN WILD-TYPE       6       10         1        2
D21V7, multiclass
           clus
vv          19P GAIN CNV 19P GAIN WILD-TYPE
  STAGE I              2                  6
  STAGE II             2                 10
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(22) Variable = 19q gain
D22V1, survival
                    sevent
clus2                 0  1
  19Q GAIN CNV        4  0
  19Q GAIN WILD-TYPE 18  2
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 4                 20 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 0                  2 
$`19Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8423 TCGA-KN-8426 TCGA-KO-8409 
      142.52        25.91         3.52        80.38 

$`19Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
      102.77        28.08         8.12        51.02       114.18        23.47 
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-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 
       20.91        75.72 

      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              3.52               0.56 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
            142.52             114.18 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
            53.145             43.985 
[1] "3.5 - 142.5 (53.1)" "0.6 - 114.2 (44.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
[1] "hr="     "2.4e+08"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          1    4
  19Q GAIN WILD-TYPE   10   10
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  FEMALE            1                 10
  MALE              4                 10
                    vv
clus                 M0 M1 MX
  19Q GAIN CNV        1  1  1
  19Q GAIN WILD-TYPE  1  1  2
D22V4, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  19Q GAIN CNV        4  0  1
  19Q GAIN WILD-TYPE  9  2  9
D22V5, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  N0            4                  9
  N1            0                  2
  NX            1                  9
D22V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN CNV             2        2         0        1
  19Q GAIN WILD-TYPE       6       10         2        2
D22V7, multiclass
           clus
vv          19Q GAIN CNV 19Q GAIN WILD-TYPE
  STAGE I              2                  6
  STAGE II             2                 10
  STAGE III            0                  2
  STAGE IV             1                  2

Clustering(23) Variable = 20p gain
D23V1, survival
                    sevent
clus2                 0  1
  20P GAIN CNV        6  0
  20P GAIN WILD-TYPE 16  2
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 6                 18 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 0                  2 
$`20P GAIN CNV`
TCGA-KM-8438 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8433 TCGA-KO-8409 
      142.52        25.91        72.69         0.56        11.21        80.38 

$`20P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
      102.77        28.08         8.12        51.02       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19         3.52        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 

      20P GAIN CNV 20P GAIN WILD-TYPE 
              0.56               2.50 
      20P GAIN CNV 20P GAIN WILD-TYPE 
            142.52             114.18 
      20P GAIN CNV 20P GAIN WILD-TYPE 
            49.300             43.985 
[1] "0.6 - 142.5 (49.3)" "2.5 - 114.2 (44.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
[1] "hr="     "2.8e+08"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          2    5
  20P GAIN WILD-TYPE    9    9
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  20P GAIN CNV        1  0  1
  20P GAIN WILD-TYPE  1  2  2
D23V4, multiclass
[1] "Remove cluster labels:" "20P GAIN CNV"          
clus
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 2                  5 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8439 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KN-8426 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
                    vv
clus                 N0 N1 NX
  20P GAIN CNV        5  1  1
  20P GAIN WILD-TYPE  8  1  9
D23V5, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  N0            5                  8
  N1            1                  1
  NX            1                  9
D23V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN CNV             3        2         1        1
  20P GAIN WILD-TYPE       5       10         1        2
D23V7, multiclass
           clus
vv          20P GAIN CNV 20P GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             2                 10
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(24) Variable = 20q gain
D24V1, survival
                    sevent
clus2                 0  1
  20Q GAIN CNV        6  0
  20Q GAIN WILD-TYPE 16  2
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 6                 18 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 0                  2 
$`20Q GAIN CNV`
TCGA-KM-8438 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8433 TCGA-KO-8409 
      142.52        25.91        72.69         0.56        11.21        80.38 

$`20Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
      102.77        28.08         8.12        51.02       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19         3.52        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 

      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              0.56               2.50 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
            142.52             114.18 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
            49.300             43.985 
[1] "0.6 - 142.5 (49.3)" "2.5 - 114.2 (44.0)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
[1] "hr="     "2.8e+08"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          2    5
  20Q GAIN WILD-TYPE    9    9
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  FEMALE            2                  9
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  20Q GAIN CNV        1  0  1
  20Q GAIN WILD-TYPE  1  2  2
D24V4, multiclass
[1] "Remove cluster labels:" "20Q GAIN CNV"          
clus
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 2                  5 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8439 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KN-8426 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
                    vv
clus                 N0 N1 NX
  20Q GAIN CNV        5  1  1
  20Q GAIN WILD-TYPE  8  1  9
D24V5, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  N0            5                  8
  N1            1                  1
  NX            1                  9
D24V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN CNV             3        2         1        1
  20Q GAIN WILD-TYPE       5       10         1        2
D24V7, multiclass
           clus
vv          20Q GAIN CNV 20Q GAIN WILD-TYPE
  STAGE I              3                  5
  STAGE II             2                 10
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(25) Variable = 22q gain
D25V1, survival
                    sevent
clus2                 0  1
  22Q GAIN CNV        6  1
  22Q GAIN WILD-TYPE 16  1
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 7                 17 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                  1 
$`22Q GAIN CNV`
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 
       80.38 

$`22Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        51.02       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 
       87.91        25.48        65.19        72.69        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        36.95        89.65        20.91        75.72 

      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              0.56               2.50 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
             80.38             142.52 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
             23.47              65.19 
[1] "0.6 - 80.4 (23.5)"  "2.5 - 142.5 (65.2)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "22Q GAIN CNV"       "22Q GAIN CNV"       "22Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "22Q GAIN CNV"       "22Q GAIN CNV"       "22Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
      "22Q GAIN CNV"       "22Q GAIN CNV"       "22Q GAIN CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
[1] "hr=" "5.2"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          1    6
  22Q GAIN WILD-TYPE   10    8
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  FEMALE            1                 10
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  22Q GAIN CNV        1  1  0
  22Q GAIN WILD-TYPE  1  1  3
D25V4, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 2                  5 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 N0 N1 NX
  22Q GAIN CNV        4  1  2
  22Q GAIN WILD-TYPE  9  1  8
D25V5, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  N0            4                  9
  N1            1                  1
  NX            2                  8
D25V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN CNV             1        3         1        2
  22Q GAIN WILD-TYPE       7        9         1        1
D25V7, multiclass
           clus
vv          22Q GAIN CNV 22Q GAIN WILD-TYPE
  STAGE I              1                  7
  STAGE II             3                  9
  STAGE III            1                  1
  STAGE IV             2                  1

Clustering(26) Variable = Xq gain
D26V1, survival
                   sevent
clus2                0  1
  XQ GAIN CNV        4  0
  XQ GAIN WILD-TYPE 18  2
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                4                20 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                0                 2 
$`XQ GAIN CNV`
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KO-8409 
       23.47        25.91         3.52        80.38 

$`XQ GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        51.02       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-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 
       20.91        75.72 

      XQ GAIN CNV XQ GAIN WILD-TYPE 
             3.52              0.56 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
            80.38            142.52 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
           24.690            51.645 
[1] "3.5 - 80.4 (24.7)"  "0.6 - 142.5 (51.6)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
[1] "hr="     "7.5e+07"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          0    5
  XQ GAIN WILD-TYPE   11    9
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  FEMALE           0                11
  MALE             5                 9
                   vv
clus                M0 M1 MX
  XQ GAIN CNV        1  1  0
  XQ GAIN WILD-TYPE  1  1  3
D26V4, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                2                 5 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-KM-8477 
"XQ GAIN WILD-TYPE" 
                   vv
clus                N0 N1 NX
  XQ GAIN CNV        4  0  1
  XQ GAIN WILD-TYPE  9  2  9
D26V5, multiclass
    clus
vv   XQ GAIN CNV XQ GAIN WILD-TYPE
  N0           4                 9
  N1           0                 2
  NX           1                 9
D26V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN CNV             2        2         0        1
  XQ GAIN WILD-TYPE       6       10         2        2
D26V7, multiclass
           clus
vv          XQ GAIN CNV XQ GAIN WILD-TYPE
  STAGE I             2                 6
  STAGE II            2                10
  STAGE III           0                 2
  STAGE IV            1                 2

Clustering(27) Variable = 1p loss
D27V1, survival
                   sevent
clus2                0  1
  1P LOSS CNV       13  1
  1P LOSS WILD-TYPE  9  1
      1P LOSS CNV 1P LOSS WILD-TYPE 
               14                10 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                 1 
$`1P LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19        72.69        67.82        23.41         2.50        36.95 
TCGA-KN-8435 TCGA-KN-8436 
       89.65        20.91 

$`1P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
        8.12        51.02        23.47        25.91         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
       52.27        11.21        75.72        80.38 

      1P LOSS CNV 1P LOSS WILD-TYPE 
             2.50              0.56 
      1P LOSS CNV 1P LOSS WILD-TYPE 
           142.52             80.38 
      1P LOSS CNV 1P LOSS WILD-TYPE 
           66.505            24.690 
[1] "2.5 - 142.5 (66.5)" "0.6 - 80.4 (24.7)" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "1P LOSS CNV"       "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "1P LOSS CNV"       "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "1P LOSS CNV"       "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          9    5
  1P LOSS WILD-TYPE    2    9
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  FEMALE           9                 2
  MALE             5                 9
                   vv
clus                M0 M1 MX
  1P LOSS CNV        1  1  1
  1P LOSS WILD-TYPE  1  1  2
D27V4, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  1P LOSS CNV        8  1  5
  1P LOSS WILD-TYPE  5  1  5
D27V5, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  N0           8                 5
  N1           1                 1
  NX           5                 5
D27V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS CNV             3        9         1        1
  1P LOSS WILD-TYPE       5        3         1        2
D27V7, multiclass
           clus
vv          1P LOSS CNV 1P LOSS WILD-TYPE
  STAGE I             3                 5
  STAGE II            9                 3
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(28) Variable = 1q loss
D28V1, survival
                   sevent
clus2                0  1
  1Q LOSS CNV       13  1
  1Q LOSS WILD-TYPE  9  1
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               14                10 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                1                 1 
$`1Q LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19        72.69        67.82        23.41         2.50        36.95 
TCGA-KN-8435 TCGA-KN-8436 
       89.65        20.91 

$`1Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
        8.12        51.02        23.47        25.91         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
       52.27        11.21        75.72        80.38 

      1Q LOSS CNV 1Q LOSS WILD-TYPE 
             2.50              0.56 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
           142.52             80.38 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
           66.505            24.690 
[1] "2.5 - 142.5 (66.5)" "0.6 - 80.4 (24.7)" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "1Q LOSS CNV"       "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV"       "1Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "1Q LOSS CNV"       "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV"       "1Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "1Q LOSS CNV"       "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV"       "1Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "1Q LOSS CNV"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          9    5
  1Q LOSS WILD-TYPE    2    9
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  FEMALE           9                 2
  MALE             5                 9
                   vv
clus                M0 M1 MX
  1Q LOSS CNV        1  1  1
  1Q LOSS WILD-TYPE  1  1  2
D28V4, multiclass
    clus
vv   1Q LOSS CNV 1Q LOSS WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  1Q LOSS CNV        8  1  5
  1Q LOSS WILD-TYPE  5  1  5
D28V5, multiclass
    clus
vv   1Q LOSS CNV 1Q LOSS WILD-TYPE
  N0           8                 5
  N1           1                 1
  NX           5                 5
D28V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS CNV             3        9         1        1
  1Q LOSS WILD-TYPE       5        3         1        2
D28V7, multiclass
           clus
vv          1Q LOSS CNV 1Q LOSS WILD-TYPE
  STAGE I             3                 5
  STAGE II            9                 3
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(29) Variable = 2p loss
D29V1, survival
                   sevent
clus2                0  1
  2P LOSS CNV       11  2
  2P LOSS WILD-TYPE 11  0
      2P LOSS CNV 2P LOSS WILD-TYPE 
               13                11 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2                 0 
$`2P LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 
      102.77        28.08       142.52       114.18        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 
       20.91 

$`2P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
        8.12        51.02        23.47        87.91        25.48        25.91 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
        3.52         0.56        11.21        75.72        80.38 

      2P LOSS CNV 2P LOSS WILD-TYPE 
             2.50              0.56 
      2P LOSS CNV 2P LOSS WILD-TYPE 
           142.52             87.91 
      2P LOSS CNV 2P LOSS WILD-TYPE 
            65.19             25.48 
[1] "2.5 - 142.5 (65.2)" "0.6 - 87.9 (25.5)" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "2P LOSS CNV"       "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV"       "2P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV"       "2P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "2P LOSS CNV"       "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV"       "2P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV"       "2P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "2P LOSS CNV"       "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV"       "2P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV"       "2P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "2P LOSS CNV"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "hr="   "3e+08"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          7    6
  2P LOSS WILD-TYPE    4    8
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  FEMALE           7                 4
  MALE             6                 8
                   vv
clus                M0 M1 MX
  2P LOSS CNV        1  1  1
  2P LOSS WILD-TYPE  1  1  2
D29V4, multiclass
    clus
vv   2P LOSS CNV 2P LOSS WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  2P LOSS CNV        7  1  5
  2P LOSS WILD-TYPE  6  1  5
D29V5, multiclass
    clus
vv   2P LOSS CNV 2P LOSS WILD-TYPE
  N0           7                 6
  N1           1                 1
  NX           5                 5
D29V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS CNV             2        9         1        1
  2P LOSS WILD-TYPE       6        3         1        2
D29V7, multiclass
           clus
vv          2P LOSS CNV 2P LOSS WILD-TYPE
  STAGE I             2                 6
  STAGE II            9                 3
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(30) Variable = 2q loss
D30V1, survival
                   sevent
clus2                0  1
  2Q LOSS CNV       11  2
  2Q LOSS WILD-TYPE 11  0
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
               13                11 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2                 0 
$`2Q LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 
      102.77        28.08       142.52       114.18        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 
       20.91 

$`2Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
        8.12        51.02        23.47        87.91        25.48        25.91 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
        3.52         0.56        11.21        75.72        80.38 

      2Q LOSS CNV 2Q LOSS WILD-TYPE 
             2.50              0.56 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
           142.52             87.91 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
            65.19             25.48 
[1] "2.5 - 142.5 (65.2)" "0.6 - 87.9 (25.5)" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "2Q LOSS CNV"       "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV"       "2Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV"       "2Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "2Q LOSS CNV"       "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV"       "2Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV"       "2Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "2Q LOSS CNV"       "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV"       "2Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV"       "2Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "2Q LOSS CNV"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "hr="   "3e+08"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          7    6
  2Q LOSS WILD-TYPE    4    8
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  FEMALE           7                 4
  MALE             6                 8
                   vv
clus                M0 M1 MX
  2Q LOSS CNV        1  1  1
  2Q LOSS WILD-TYPE  1  1  2
D30V4, multiclass
    clus
vv   2Q LOSS CNV 2Q LOSS WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  2Q LOSS CNV        7  1  5
  2Q LOSS WILD-TYPE  6  1  5
D30V5, multiclass
    clus
vv   2Q LOSS CNV 2Q LOSS WILD-TYPE
  N0           7                 6
  N1           1                 1
  NX           5                 5
D30V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS CNV             2        9         1        1
  2Q LOSS WILD-TYPE       6        3         1        2
D30V7, multiclass
           clus
vv          2Q LOSS CNV 2Q LOSS WILD-TYPE
  STAGE I             2                 6
  STAGE II            9                 3
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(31) Variable = 3p loss
D31V1, survival
                   sevent
clus2                0  1
  3P LOSS CNV        4  0
  3P LOSS WILD-TYPE 18  2
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4                20 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                0                 2 
$`3P LOSS CNV`
TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 
       87.91        72.69         2.50        20.91 

$`3P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        51.02       114.18 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 
       23.47        25.48        25.91        65.19         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82        23.41        11.21        36.95        89.65 
TCGA-KN-8437 TCGA-KO-8409 
       75.72        80.38 

      3P LOSS CNV 3P LOSS WILD-TYPE 
             2.50              0.56 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            87.91            142.52 
      3P LOSS CNV 3P LOSS WILD-TYPE 
           46.800            43.985 
[1] "2.5 - 87.9 (46.8)"  "0.6 - 142.5 (44.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr="     "2.4e+08"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          2    2
  3P LOSS WILD-TYPE    9   12
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  FEMALE           2                 9
  MALE             2                12
                   vv
clus                M0 M1 MX
  3P LOSS CNV        0  0  0
  3P LOSS WILD-TYPE  2  2  3
D31V4, multiclass
                   vv
clus                N0 N1 NX
  3P LOSS CNV        2  0  2
  3P LOSS WILD-TYPE 11  2  8
D31V5, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  N0           2                11
  N1           0                 2
  NX           2                 8
D31V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS CNV             1        3         0        0
  3P LOSS WILD-TYPE       7        9         2        3
D31V7, multiclass
           clus
vv          3P LOSS CNV 3P LOSS WILD-TYPE
  STAGE I             1                 7
  STAGE II            3                 9
  STAGE III           0                 2
  STAGE IV            0                 3

Clustering(32) Variable = 3q loss
D32V1, survival
                   sevent
clus2                0  1
  3Q LOSS CNV        4  0
  3Q LOSS WILD-TYPE 18  2
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                4                20 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                0                 2 
$`3Q LOSS CNV`
TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 
       87.91        72.69         2.50        20.91 

$`3Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        51.02       114.18 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 
       23.47        25.48        25.91        65.19         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        67.82        23.41        11.21        36.95        89.65 
TCGA-KN-8437 TCGA-KO-8409 
       75.72        80.38 

      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             2.50              0.56 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            87.91            142.52 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
           46.800            43.985 
[1] "2.5 - 87.9 (46.8)"  "0.6 - 142.5 (44.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr="     "2.4e+08"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          2    2
  3Q LOSS WILD-TYPE    9   12
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  FEMALE           2                 9
  MALE             2                12
                   vv
clus                M0 M1 MX
  3Q LOSS CNV        0  0  0
  3Q LOSS WILD-TYPE  2  2  3
D32V4, multiclass
                   vv
clus                N0 N1 NX
  3Q LOSS CNV        2  0  2
  3Q LOSS WILD-TYPE 11  2  8
D32V5, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  N0           2                11
  N1           0                 2
  NX           2                 8
D32V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS CNV             1        3         0        0
  3Q LOSS WILD-TYPE       7        9         2        3
D32V7, multiclass
           clus
vv          3Q LOSS CNV 3Q LOSS WILD-TYPE
  STAGE I             1                 7
  STAGE II            3                 9
  STAGE III           0                 2
  STAGE IV            0                 3

Clustering(33) Variable = 6p loss
D33V1, survival
                   sevent
clus2                0  1
  6P LOSS CNV       13  2
  6P LOSS WILD-TYPE  9  0
      6P LOSS CNV 6P LOSS WILD-TYPE 
               15                 9 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                2                 0 
$`6P LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19        72.69        52.27        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       36.95        89.65        20.91 

$`6P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
        8.12        51.02        23.47        25.91         3.52         0.56 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
       11.21        75.72        80.38 

      6P LOSS CNV 6P LOSS WILD-TYPE 
             2.50              0.56 
      6P LOSS CNV 6P LOSS WILD-TYPE 
           142.52             80.38 
      6P LOSS CNV 6P LOSS WILD-TYPE 
            65.19             23.47 
[1] "2.5 - 142.5 (65.2)" "0.6 - 80.4 (23.5)" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "6P LOSS CNV"       "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV"       "6P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV"       "6P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "6P LOSS CNV"       "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV"       "6P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV"       "6P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "6P LOSS CNV"       "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV"       "6P LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV"       "6P LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "6P LOSS CNV"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr="     "2.6e+08"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          9    6
  6P LOSS WILD-TYPE    2    8
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  FEMALE           9                 2
  MALE             6                 8
                   vv
clus                M0 M1 MX
  6P LOSS CNV        1  1  1
  6P LOSS WILD-TYPE  1  1  2
D33V4, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  6P LOSS CNV        9  1  5
  6P LOSS WILD-TYPE  4  1  5
D33V5, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  N0           9                 4
  N1           1                 1
  NX           5                 5
D33V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS CNV             3       10         1        1
  6P LOSS WILD-TYPE       5        2         1        2
D33V7, multiclass
           clus
vv          6P LOSS CNV 6P LOSS WILD-TYPE
  STAGE I             3                 5
  STAGE II           10                 2
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(34) Variable = 6q loss
D34V1, survival
                   sevent
clus2                0  1
  6Q LOSS CNV       13  2
  6Q LOSS WILD-TYPE  9  0
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               15                 9 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                2                 0 
$`6Q LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19        72.69        52.27        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       36.95        89.65        20.91 

$`6Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
        8.12        51.02        23.47        25.91         3.52         0.56 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
       11.21        75.72        80.38 

      6Q LOSS CNV 6Q LOSS WILD-TYPE 
             2.50              0.56 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
           142.52             80.38 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            65.19             23.47 
[1] "2.5 - 142.5 (65.2)" "0.6 - 80.4 (23.5)" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "6Q LOSS CNV"       "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV"       "6Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV"       "6Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "6Q LOSS CNV"       "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV"       "6Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV"       "6Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "6Q LOSS CNV"       "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV"       "6Q LOSS CNV" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV"       "6Q LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "6Q LOSS CNV"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr="     "2.6e+08"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          9    6
  6Q LOSS WILD-TYPE    2    8
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  FEMALE           9                 2
  MALE             6                 8
                   vv
clus                M0 M1 MX
  6Q LOSS CNV        1  1  1
  6Q LOSS WILD-TYPE  1  1  2
D34V4, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  M0           1                 1
  M1           1                 1
  MX           1                 2
                   vv
clus                N0 N1 NX
  6Q LOSS CNV        9  1  5
  6Q LOSS WILD-TYPE  4  1  5
D34V5, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  N0           9                 4
  N1           1                 1
  NX           5                 5
D34V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS CNV             3       10         1        1
  6Q LOSS WILD-TYPE       5        2         1        2
D34V7, multiclass
           clus
vv          6Q LOSS CNV 6Q LOSS WILD-TYPE
  STAGE I             3                 5
  STAGE II           10                 2
  STAGE III           1                 1
  STAGE IV            1                 2

Clustering(35) Variable = 8p loss
D35V1, survival
                   sevent
clus2                0  1
  8P LOSS CNV        3  0
  8P LOSS WILD-TYPE 19  2
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3                21 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                0                 2 
$`8P LOSS CNV`
TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
        2.50        89.65        20.91 

$`8P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        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-8433 
        3.52         0.56        52.27        67.82        23.41        11.21 
TCGA-KN-8434 TCGA-KN-8437 TCGA-KO-8409 
       36.95        75.72        80.38 

      8P LOSS CNV 8P LOSS WILD-TYPE 
             2.50              0.56 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            89.65            142.52 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            20.91             51.02 
[1] "2.5 - 89.7 (20.9)"  "0.6 - 142.5 (51.0)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr="     "7.5e+07"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          1    2
  8P LOSS WILD-TYPE   10   12
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  FEMALE           1                10
  MALE             2                12
                   vv
clus                M0 M1 MX
  8P LOSS CNV        0  0  0
  8P LOSS WILD-TYPE  2  2  3
D35V4, multiclass
                   vv
clus                N0 N1 NX
  8P LOSS CNV        0  0  3
  8P LOSS WILD-TYPE 13  2  7
D35V5, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  N0           0                13
  N1           0                 2
  NX           3                 7
D35V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS CNV             0        3         0        0
  8P LOSS WILD-TYPE       8        9         2        3
D35V7, multiclass
           clus
vv          8P LOSS CNV 8P LOSS WILD-TYPE
  STAGE I             0                 8
  STAGE II            3                 9
  STAGE III           0                 2
  STAGE IV            0                 3

Clustering(36) Variable = 10p loss
D36V1, survival
                    sevent
clus2                 0  1
  10P LOSS CNV       10  2
  10P LOSS WILD-TYPE 12  0
      10P LOSS CNV 10P LOSS WILD-TYPE 
                12                 12 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 2                  0 
$`10P LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
      102.77        28.08       114.18        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       72.69        52.27        67.82         2.50        36.95        89.65 

$`10P LOSS WILD-TYPE`
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 
      142.52         8.12        51.02        23.47        25.91         3.52 
TCGA-KN-8427 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8409 
        0.56        23.41        11.21        20.91        75.72        80.38 

      10P LOSS CNV 10P LOSS WILD-TYPE 
              2.50               0.56 
      10P LOSS CNV 10P LOSS WILD-TYPE 
            114.18             142.52 
      10P LOSS CNV 10P LOSS WILD-TYPE 
            66.505             23.440 
[1] "2.5 - 114.2 (66.5)" "0.6 - 142.5 (23.4)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"10P LOSS WILD-TYPE"       "10P LOSS CNV"       "10P LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr="   "3e+08"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          7    5
  10P LOSS WILD-TYPE    4    9
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  FEMALE            7                  4
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  10P LOSS CNV        1  1  0
  10P LOSS WILD-TYPE  1  1  3
D36V4, multiclass
[1] "Remove cluster labels:" "10P LOSS CNV"          
clus
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 2                  5 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8477 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-KN-8426         TCGA-KO-8409 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
                    vv
clus                 N0 N1 NX
  10P LOSS CNV        8  1  3
  10P LOSS WILD-TYPE  5  1  7
D36V5, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  N0            8                  5
  N1            1                  1
  NX            3                  7
D36V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS CNV             3        7         1        1
  10P LOSS WILD-TYPE       5        5         1        2
D36V7, multiclass
           clus
vv          10P LOSS CNV 10P LOSS WILD-TYPE
  STAGE I              3                  5
  STAGE II             7                  5
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(37) Variable = 10q loss
D37V1, survival
                    sevent
clus2                 0  1
  10Q LOSS CNV       10  2
  10Q LOSS WILD-TYPE 12  0
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                12                 12 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 2                  0 
$`10Q LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
      102.77        28.08       114.18        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       72.69        52.27        67.82         2.50        36.95        89.65 

$`10Q LOSS WILD-TYPE`
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 
      142.52         8.12        51.02        23.47        25.91         3.52 
TCGA-KN-8427 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8409 
        0.56        23.41        11.21        20.91        75.72        80.38 

      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              2.50               0.56 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
            114.18             142.52 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
            66.505             23.440 
[1] "2.5 - 114.2 (66.5)" "0.6 - 142.5 (23.4)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr="   "3e+08"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          7    5
  10Q LOSS WILD-TYPE    4    9
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  FEMALE            7                  4
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  10Q LOSS CNV        1  1  0
  10Q LOSS WILD-TYPE  1  1  3
D37V4, multiclass
[1] "Remove cluster labels:" "10Q LOSS CNV"          
clus
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 2                  5 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8477 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-KN-8426         TCGA-KO-8409 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
                    vv
clus                 N0 N1 NX
  10Q LOSS CNV        8  1  3
  10Q LOSS WILD-TYPE  5  1  7
D37V5, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  N0            8                  5
  N1            1                  1
  NX            3                  7
D37V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS CNV             3        7         1        1
  10Q LOSS WILD-TYPE       5        5         1        2
D37V7, multiclass
           clus
vv          10Q LOSS CNV 10Q LOSS WILD-TYPE
  STAGE I              3                  5
  STAGE II             7                  5
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(38) Variable = 13q loss
D38V1, survival
                    sevent
clus2                 0  1
  13Q LOSS CNV       11  2
  13Q LOSS WILD-TYPE 11  0
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                13                 11 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                  0 
$`13Q LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
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 
       89.65 

$`13Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
        8.12        51.02        23.47        25.91        65.19         3.52 
TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8409 
        0.56        11.21        20.91        75.72        80.38 

      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              2.50               0.56 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
            142.52              80.38 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             67.82              23.47 
[1] "2.5 - 142.5 (67.8)" "0.6 - 80.4 (23.5)" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr="   "3e+08"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          8    5
  13Q LOSS WILD-TYPE    3    9
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  FEMALE            8                  3
  MALE              5                  9
                    vv
clus                 M0 M1 MX
  13Q LOSS CNV        1  1  1
  13Q LOSS WILD-TYPE  1  1  2
D38V4, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  13Q LOSS CNV        8  1  4
  13Q LOSS WILD-TYPE  5  1  6
D38V5, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  N0            8                  5
  N1            1                  1
  NX            4                  6
D38V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS CNV             2        9         1        1
  13Q LOSS WILD-TYPE       6        3         1        2
D38V7, multiclass
           clus
vv          13Q LOSS CNV 13Q LOSS WILD-TYPE
  STAGE I              2                  6
  STAGE II             9                  3
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(39) Variable = 17p loss
D39V1, survival
                    sevent
clus2                 0  1
  17P LOSS CNV       13  2
  17P LOSS WILD-TYPE  9  0
      17P LOSS CNV 17P LOSS WILD-TYPE 
                15                  9 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 2                  0 
$`17P LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19        72.69        52.27        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       36.95        89.65        20.91 

$`17P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
        8.12        51.02        23.47        25.91         3.52         0.56 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
       11.21        75.72        80.38 

      17P LOSS CNV 17P LOSS WILD-TYPE 
              2.50               0.56 
      17P LOSS CNV 17P LOSS WILD-TYPE 
            142.52              80.38 
      17P LOSS CNV 17P LOSS WILD-TYPE 
             65.19              23.47 
[1] "2.5 - 142.5 (65.2)" "0.6 - 80.4 (23.5)" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr="     "2.6e+08"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          9    6
  17P LOSS WILD-TYPE    2    8
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  FEMALE            9                  2
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  17P LOSS CNV        1  1  1
  17P LOSS WILD-TYPE  1  1  2
D39V4, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  17P LOSS CNV        9  1  5
  17P LOSS WILD-TYPE  4  1  5
D39V5, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  N0            9                  4
  N1            1                  1
  NX            5                  5
D39V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS CNV             3       10         1        1
  17P LOSS WILD-TYPE       5        2         1        2
D39V7, multiclass
           clus
vv          17P LOSS CNV 17P LOSS WILD-TYPE
  STAGE I              3                  5
  STAGE II            10                  2
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(40) Variable = 17q loss
D40V1, survival
                    sevent
clus2                 0  1
  17Q LOSS CNV       13  2
  17Q LOSS WILD-TYPE  9  0
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                15                  9 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 2                  0 
$`17Q LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19        72.69        52.27        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       36.95        89.65        20.91 

$`17Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
        8.12        51.02        23.47        25.91         3.52         0.56 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8409 
       11.21        75.72        80.38 

      17Q LOSS CNV 17Q LOSS WILD-TYPE 
              2.50               0.56 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
            142.52              80.38 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             65.19              23.47 
[1] "2.5 - 142.5 (65.2)" "0.6 - 80.4 (23.5)" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "17Q LOSS CNV"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "17Q LOSS CNV"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "17Q LOSS CNV"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "17Q LOSS CNV"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "17Q LOSS CNV"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "17Q LOSS CNV"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr="     "2.6e+08"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          9    6
  17Q LOSS WILD-TYPE    2    8
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  FEMALE            9                  2
  MALE              6                  8
                    vv
clus                 M0 M1 MX
  17Q LOSS CNV        1  1  1
  17Q LOSS WILD-TYPE  1  1  2
D40V4, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  M0            1                  1
  M1            1                  1
  MX            1                  2
                    vv
clus                 N0 N1 NX
  17Q LOSS CNV        9  1  5
  17Q LOSS WILD-TYPE  4  1  5
D40V5, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  N0            9                  4
  N1            1                  1
  NX            5                  5
D40V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS CNV             3       10         1        1
  17Q LOSS WILD-TYPE       5        2         1        2
D40V7, multiclass
           clus
vv          17Q LOSS CNV 17Q LOSS WILD-TYPE
  STAGE I              3                  5
  STAGE II            10                  2
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(41) Variable = 18q loss
D41V1, survival
                    sevent
clus2                 0  1
  18Q LOSS CNV        3  0
  18Q LOSS WILD-TYPE 19  2
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 3                 21 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 0                  2 
$`18Q LOSS CNV`
TCGA-KL-8328 TCGA-KN-8424 TCGA-KN-8429 
      102.77        65.19        67.82 

$`18Q LOSS WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
       28.08       142.52         8.12        51.02       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       87.91        25.48        25.91        72.69         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        23.41         2.50        11.21        36.95        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8409 
       20.91        75.72        80.38 

      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             65.19               0.56 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
            102.77             142.52 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             67.82              28.08 
[1] "65.2 - 102.8 (67.8)" "0.6 - 142.5 (28.1)" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr="     "2.8e+08"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          2    1
  18Q LOSS WILD-TYPE    9   13
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  FEMALE            2                  9
  MALE              1                 13
                    vv
clus                 M0 M1 MX
  18Q LOSS CNV        1  0  0
  18Q LOSS WILD-TYPE  1  2  3
D41V4, multiclass
[1] "Remove cluster labels:" "18Q LOSS CNV"          
clus
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 1                  6 
        TCGA-KL-8339         TCGA-KM-8438         TCGA-KM-8439 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KM-8477         TCGA-KN-8426         TCGA-KO-8409 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
                    vv
clus                 N0 N1 NX
  18Q LOSS CNV        3  0  0
  18Q LOSS WILD-TYPE 10  2 10
D41V5, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  N0            3                 10
  N1            0                  2
  NX            0                 10
D41V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS CNV             1        1         1        0
  18Q LOSS WILD-TYPE       7       11         1        3
D41V7, multiclass
           clus
vv          18Q LOSS CNV 18Q LOSS WILD-TYPE
  STAGE I              1                  7
  STAGE II             1                 11
  STAGE III            1                  1
  STAGE IV             0                  3

Clustering(42) Variable = 21q loss
D42V1, survival
                    sevent
clus2                 0  1
  21Q LOSS CNV        7  2
  21Q LOSS WILD-TYPE 15  0
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 9                 15 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                  0 
$`21Q LOSS CNV`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 
      102.77        28.08        25.48        65.19        72.69        52.27 
TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 
       67.82         2.50        36.95 

$`21Q LOSS WILD-TYPE`
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      142.52         8.12        51.02       114.18        23.47        87.91 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8435 
       25.91         3.52         0.56        23.41        11.21        89.65 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8409 
       20.91        75.72        80.38 

      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              2.50               0.56 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
            102.77             142.52 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
             52.27              25.91 
[1] "2.5 - 102.8 (52.3)" "0.6 - 142.5 (25.9)"
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KM-8438 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8477         TCGA-KN-8418 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-KN-8426         TCGA-KN-8427         TCGA-KN-8428 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8429         TCGA-KN-8431         TCGA-KN-8432 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-KN-8433         TCGA-KN-8434         TCGA-KN-8435 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8436         TCGA-KN-8437         TCGA-KO-8409 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr="     "1.8e+09"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          5    4
  21Q LOSS WILD-TYPE    6   10
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  FEMALE            5                  6
  MALE              4                 10
                    vv
clus                 M0 M1 MX
  21Q LOSS CNV        1  1  0
  21Q LOSS WILD-TYPE  1  1  3
D42V4, multiclass
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                  5 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8477 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-KN-8426         TCGA-KO-8409 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
                    vv
clus                 N0 N1 NX
  21Q LOSS CNV        6  1  2
  21Q LOSS WILD-TYPE  7  1  8
D42V5, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  N0            6                  7
  N1            1                  1
  NX            2                  8
D42V6, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS CNV             3        4         1        1
  21Q LOSS WILD-TYPE       5        8         1        2
D42V7, multiclass
           clus
vv          21Q LOSS CNV 21Q LOSS WILD-TYPE
  STAGE I              3                  5
  STAGE II             4                  8
  STAGE III            1                  1
  STAGE IV             1                  2

Clustering(43) Variable = Xq loss
D43V1, survival
                   sevent
clus2                0  1
  XQ LOSS CNV        9  0
  XQ LOSS WILD-TYPE 13  2
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                9                15 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                0                 2 
$`XQ LOSS CNV`
TCGA-KL-8328 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 
      102.77       114.18        87.91        65.19        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
        2.50        89.65        20.91 

$`XQ LOSS WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8422 
       28.08       142.52         8.12        51.02        23.47        25.48 
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-KN-8434 TCGA-KN-8437 TCGA-KO-8409 
       36.95        75.72        80.38 

      XQ LOSS CNV XQ LOSS WILD-TYPE 
             2.50              0.56 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
           114.18            142.52 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            67.82             28.08 
[1] "2.5 - 114.2 (67.8)" "0.6 - 142.5 (28.1)"
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KM-8477        TCGA-KN-8418        TCGA-KN-8419        TCGA-KN-8421 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424        TCGA-KN-8425 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8426        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-KN-8431        TCGA-KN-8432        TCGA-KN-8433        TCGA-KN-8434 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8435        TCGA-KN-8436        TCGA-KN-8437        TCGA-KO-8409 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr="     "1.6e+09"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          6    3
  XQ LOSS WILD-TYPE    5   11
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  FEMALE           6                 5
  MALE             3                11
                   vv
clus                M0 M1 MX
  XQ LOSS CNV        1  0  0
  XQ LOSS WILD-TYPE  1  2  3
D43V4, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                1                 6 
       TCGA-KL-8339        TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8477 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KN-8426        TCGA-KO-8409 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                   vv
clus                N0 N1 NX
  XQ LOSS CNV        5  0  4
  XQ LOSS WILD-TYPE  8  2  6
D43V5, multiclass
    clus
vv   XQ LOSS CNV XQ LOSS WILD-TYPE
  N0           5                 8
  N1           0                 2
  NX           4                 6
D43V6, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS CNV             1        7         1        0
  XQ LOSS WILD-TYPE       7        5         1        3
D43V7, multiclass
           clus
vv          XQ LOSS CNV XQ LOSS WILD-TYPE
  STAGE I             1                 7
  STAGE II            7                 5
  STAGE III           1                 1
  STAGE IV            0                 3
                   V1.D                      V2                      V3 
        "Time to Death"                   "AGE"                "GENDER" 
                     V4                      V5                      V6 
   "DISTANT.METASTASIS" "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE" 
                     V7 
"NEOPLASM.DISEASESTAGE" 
> q(save="no")
