
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/4427011/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/ESCA-TP/4396310/ESCA-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=ESCA-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=ESCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/ESCA-TP/4396310/ESCA-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/4427011/transformed.cor.cli.txt"

nPatients in clinical file=19, in cluster file=63, common to both=19
[1] "Reduce the number of clustering variables from 80 to 54."
[1] 54 19
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6                13 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6                13 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                11 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                11 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                12 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                12 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                16 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                16 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                15 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                15 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11                 8 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11                 8 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                12 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                12 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                15 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                15 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               13                 6 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               13                 6 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               10                 9 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               10                 9 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                13 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11                 8 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11                 8 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                16 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                16 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 14 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 14 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 16 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 16 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 14 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 14 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 13 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 13 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 14 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 14 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 15 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 15 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 15 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 15 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 14 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 14 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 14 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 14 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 15 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 15 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 13 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 13 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                15                  4 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                15                  4 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                  3 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                  3 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 14 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 14 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                13 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                10 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                 9 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                 9 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                12 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                12 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5                14 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5                14 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                 9 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                 9 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                11 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                11 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               10                 9 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               10                 9 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9                10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                9                10 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                 14 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                 14 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                 13 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                 13 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 14 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 14 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 12 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 12 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 15 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 15 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 16 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 16 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                  9 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                  9 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                 15 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                 15 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 14 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 14 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 16 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 16 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                 16 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                 16 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                 12 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                 12 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 15 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 15 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 11 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 11 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 11 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 11 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 14 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 14 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                11                  8 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                11                  8 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 11 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 11 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"          "VITALSTATUS"           "DAYSTODEATH"          
 [4] "DAYSTOLASTFOLLOWUP"    "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
 [7] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "DCCUPLOADDATE"        
[10] "GENDER"                "NUMBERPACKYEARSSMOKED" "BATCHNUMBER"          

Input Data has 12 rows and 19 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D 
          NA           NA           NA            1            8           NA 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
         106          112          124           NA          101           NA 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
          NA          934          882           NA           NA            4 
TCGA-LN-A4A9 
           2 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "NUMBERPACKYEARSSMOKED"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 19 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 4  7  6  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    4     7     8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 4  7  6  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    4     7     8 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
 7  9  2  1 
[1] "table(vv)"
vv
      N0 N1+N2+N3 
       7       12 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
 7  9  2  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 7

$Class1_nSamples
[1] 12

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2+N3"


      N0 N1+N2+N3 
       7       12 
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2               0 1
  1P GAIN MUTATED   3 2
  1P GAIN WILD-TYPE 7 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                 3 
$`1P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OX TCGA-LN-A4A2 
        0.03         4.08        18.35         7.43         0.13 

$`1P GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.26         3.48         3.68         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
       30.71        29.00         7.10         0.07 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            18.35             30.71 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             4.08              3.40 
[1] "0.0 - 18.4 (4.1)" "0.1 - 30.7 (3.4)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  1P GAIN MUTATED          1         1         4          0          0
  1P GAIN WILD-TYPE        1         2         3          4          2
                   vv
clus                STAGE IIIC
  1P GAIN MUTATED            0
  1P GAIN WILD-TYPE          1
D1V3, multiclass
                   vv
clus                T1 T2 T3+T4
  1P GAIN MUTATED    2  3     1
  1P GAIN WILD-TYPE  2  4     7
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                  2                 2
  T2                  3                 4
  T3+T4               1                 7
                   vv
clus                N0 N1+N2+N3
  1P GAIN MUTATED    2        4
  1P GAIN WILD-TYPE  5        8
D1V5, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                     2                 5
  N1+N2+N3               4                 8
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  5
  1P GAIN WILD-TYPE  2 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    5
  1P GAIN WILD-TYPE    2   11
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                 2
  MALE                 5                11
D1V7, continuous

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2               0 1
  1Q GAIN MUTATED   4 2
  1Q GAIN WILD-TYPE 6 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                 9 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                 3 
$`1Q GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OX TCGA-LN-A4A2 
        0.03         3.68         4.08        18.35         7.43         0.13 

$`1Q GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.26         3.48         3.32         1.38         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
       29.00         7.10         0.07 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            18.35             30.71 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             3.88              3.32 
[1] "0.0 - 18.4 (3.9)" "0.1 - 30.7 (3.3)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  1Q GAIN MUTATED          1         1         5          1          0
  1Q GAIN WILD-TYPE        1         2         2          3          2
                   vv
clus                STAGE IIIC
  1Q GAIN MUTATED            0
  1Q GAIN WILD-TYPE          1
D2V3, multiclass
                   vv
clus                T1 T2 T3+T4
  1Q GAIN MUTATED    3  3     2
  1Q GAIN WILD-TYPE  1  4     6
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  3                 1
  T2                  3                 4
  T3+T4               2                 6
                   vv
clus                N0 N1+N2+N3
  1Q GAIN MUTATED    3        5
  1Q GAIN WILD-TYPE  4        7
D2V5, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                     3                 4
  N1+N2+N3               5                 7
D2V6, binary
                   cls
clus                0 1
  1Q GAIN MUTATED   1 7
  1Q GAIN WILD-TYPE 2 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    7
  1Q GAIN WILD-TYPE    2    9
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               1                 2
  MALE                 7                 9
D2V7, continuous

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2               0 1
  2P GAIN MUTATED   5 2
  2P GAIN WILD-TYPE 5 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                 8 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 3 
$`2P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         3.68         4.08        18.35         3.32         3.16 
TCGA-LN-A4A2 
        0.13 

$`2P GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        0.26         3.48         1.38        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.03              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            18.35             30.71 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             3.32              5.29 
[1] "0.0 - 18.4 (3.3)" "0.1 - 30.7 (5.3)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  2P GAIN MUTATED          2         1         3          0          0
  2P GAIN WILD-TYPE        0         2         4          4          2
                   vv
clus                STAGE IIIC
  2P GAIN MUTATED            1
  2P GAIN WILD-TYPE          0
D3V3, multiclass
                   vv
clus                T1 T2 T3+T4
  2P GAIN MUTATED    4  1     2
  2P GAIN WILD-TYPE  0  6     6
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                  4                 0
  T2                  1                 6
  T3+T4               2                 6
                   vv
clus                N0 N1+N2+N3
  2P GAIN MUTATED    3        4
  2P GAIN WILD-TYPE  4        8
D3V5, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                     3                 4
  N1+N2+N3               4                 8
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    1  6
  2P GAIN WILD-TYPE  2 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    6
  2P GAIN WILD-TYPE    2   10
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               1                 2
  MALE                 6                10
D3V7, continuous

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2               0 1
  2Q GAIN MUTATED   3 0
  2Q GAIN WILD-TYPE 7 5
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                12 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                0                 5 
$`2Q GAIN MUTATED`
TCGA-L5-A4OF TCGA-L5-A4OO TCGA-LN-A4A2 
        3.68         3.32         0.13 

$`2Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.03         0.26         3.48         4.08        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        3.16        30.71        29.00         7.10         7.43         0.07 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.13              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             3.68             30.71 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             3.32              3.78 
[1] "0.1 - 3.7 (3.3)"  "0.0 - 30.7 (3.8)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
[1] "hr="     "2.5e+08"
D4V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  2Q GAIN MUTATED          0         1         1          0          0
  2Q GAIN WILD-TYPE        2         2         6          4          2
                   vv
clus                STAGE IIIC
  2Q GAIN MUTATED            1
  2Q GAIN WILD-TYPE          0
D4V3, multiclass
                   vv
clus                T1 T2 T3+T4
  2Q GAIN MUTATED    1  0     2
  2Q GAIN WILD-TYPE  3  7     6
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                  1                 3
  T2                  0                 7
  T3+T4               2                 6
                   vv
clus                N0 N1+N2+N3
  2Q GAIN MUTATED    1        2
  2Q GAIN WILD-TYPE  6       10
D4V5, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                     1                 6
  N1+N2+N3               2                10
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    0  3
  2Q GAIN WILD-TYPE  3 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0    3
  2Q GAIN WILD-TYPE    3   13
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               0                 3
  MALE                 3                13
D4V7, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                11 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A4P3        TCGA-L5-A4OE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OQ        TCGA-L5-A4OU 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-LN-A4A9 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2               0 1
  3P GAIN MUTATED   3 1
  3P GAIN WILD-TYPE 7 4
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                11 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 4 
$`3P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4OR TCGA-LN-A4A9 
        0.03         4.08         3.16         0.07 

$`3P GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
       30.71        29.00         7.10         7.43         0.13 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.03              0.13 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             4.08             30.71 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            1.615             3.680 
[1] "0.0 - 4.1 (1.6)"  "0.1 - 30.7 (3.7)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
[1] "hr=" "4.2"
D5V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  3P GAIN MUTATED          2         1         1          0          0
  3P GAIN WILD-TYPE        0         2         6          4          2
                   vv
clus                STAGE IIIC
  3P GAIN MUTATED            0
  3P GAIN WILD-TYPE          1
D5V3, multiclass
                   vv
clus                T1 T2 T3+T4
  3P GAIN MUTATED    2  2     0
  3P GAIN WILD-TYPE  2  5     8
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                  2                 2
  T2                  2                 5
  T3+T4               0                 8
                   vv
clus                N0 N1+N2+N3
  3P GAIN MUTATED    3        1
  3P GAIN WILD-TYPE  4       11
D5V5, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                     3                 4
  N1+N2+N3               1                11
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  3
  3P GAIN WILD-TYPE  2 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    3
  3P GAIN WILD-TYPE    2   13
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                 2
  MALE                 3                13
D5V7, continuous

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2               0 1
  3Q GAIN MUTATED   6 2
  3Q GAIN WILD-TYPE 4 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                 7 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 3 
$`3Q GAIN MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW 
        0.03         0.26         4.08         3.32         3.16         7.10 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

$`3Q GAIN WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        3.48         3.68        18.35         1.38        30.71        29.00 
TCGA-L5-A4OX 
        7.43 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.03              1.38 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             7.10             30.71 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.71              7.43 
[1] "0.0 - 7.1 (1.7)"  "1.4 - 30.7 (7.4)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
[1] "hr=" "4.5"
D6V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  3Q GAIN MUTATED          2         2         3          2          1
  3Q GAIN WILD-TYPE        0         1         4          2          1
                   vv
clus                STAGE IIIC
  3Q GAIN MUTATED            1
  3Q GAIN WILD-TYPE          0
D6V3, multiclass
                   vv
clus                T1 T2 T3+T4
  3Q GAIN MUTATED    2  4     5
  3Q GAIN WILD-TYPE  2  3     3
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                  2                 2
  T2                  4                 3
  T3+T4               5                 3
                   vv
clus                N0 N1+N2+N3
  3Q GAIN MUTATED    5        6
  3Q GAIN WILD-TYPE  2        6
D6V5, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                     5                 2
  N1+N2+N3               6                 6
D6V6, binary
                   cls
clus                0 1
  3Q GAIN MUTATED   2 9
  3Q GAIN WILD-TYPE 1 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    9
  3Q GAIN WILD-TYPE    1    7
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                 1
  MALE                 9                 7
D6V7, continuous

Clustering(7) Variable = 5P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2               0 1
  5P GAIN MUTATED   4 2
  5P GAIN WILD-TYPE 6 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                 9 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 3 
$`5P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW 
        0.03         4.08         3.32         3.16        29.00         7.10 

$`5P GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.26         3.48         3.68        18.35         1.38        30.71 
TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.43         0.13         0.07 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            29.00             30.71 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             3.70              3.48 
[1] "0.0 - 29.0 (3.7)" "0.1 - 30.7 (3.5)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D7V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  5P GAIN MUTATED          2         1         2          1          0
  5P GAIN WILD-TYPE        0         2         5          3          2
                   vv
clus                STAGE IIIC
  5P GAIN MUTATED            1
  5P GAIN WILD-TYPE          0
D7V3, multiclass
                   vv
clus                T1 T2 T3+T4
  5P GAIN MUTATED    2  2     3
  5P GAIN WILD-TYPE  2  5     5
D7V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                  2                 2
  T2                  2                 5
  T3+T4               3                 5
                   vv
clus                N0 N1+N2+N3
  5P GAIN MUTATED    3        4
  5P GAIN WILD-TYPE  4        8
D7V5, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                     3                 4
  N1+N2+N3               4                 8
D7V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  5
  5P GAIN WILD-TYPE  1 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    5
  5P GAIN WILD-TYPE    1   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                 1
  MALE                 5                11
D7V7, continuous

Clustering(8) Variable = 6P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2               0 1
  6P GAIN MUTATED   3 1
  6P GAIN WILD-TYPE 7 4
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                11 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                 4 
$`6P GAIN MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OW 
        0.26         4.08        30.71         7.10 

$`6P GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16        29.00         7.43         0.13         0.07 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.26              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            30.71             29.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             5.59              3.32 
[1] "0.3 - 30.7 (5.6)" "0.0 - 29.0 (3.3)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D8V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  6P GAIN MUTATED          1         0         2          0          1
  6P GAIN WILD-TYPE        1         3         5          4          1
                   vv
clus                STAGE IIIC
  6P GAIN MUTATED            0
  6P GAIN WILD-TYPE          1
D8V3, multiclass
                   vv
clus                T1 T2 T3+T4
  6P GAIN MUTATED    1  2     1
  6P GAIN WILD-TYPE  3  5     7
D8V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  1                 3
  T2                  2                 5
  T3+T4               1                 7
                   vv
clus                N0 N1+N2+N3
  6P GAIN MUTATED    1        3
  6P GAIN WILD-TYPE  6        9
D8V5, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                     1                 6
  N1+N2+N3               3                 9
D8V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    3  1
  6P GAIN WILD-TYPE  0 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    1
  6P GAIN WILD-TYPE    0   15
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               3                 0
  MALE                 1                15
D8V7, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                10 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A4P3        TCGA-L5-A4OE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ        TCGA-L5-A4OU 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 

Clustering(9) Variable = 7P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2               0 1
  7P GAIN MUTATED   7 4
  7P GAIN WILD-TYPE 3 1
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               11                 4 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                 1 
$`7P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A2 
        3.16        30.71        29.00         7.10         0.13 

$`7P GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4OX TCGA-LN-A4A9 
        0.26         4.08         7.43         0.07 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            30.71              7.43 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             3.48              2.17 
[1] "0.0 - 30.7 (3.5)" "0.1 - 7.4 (2.2)" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  7P GAIN MUTATED          1         2         6          2          1
  7P GAIN WILD-TYPE        1         1         1          2          1
                   vv
clus                STAGE IIIC
  7P GAIN MUTATED            1
  7P GAIN WILD-TYPE          0
D9V3, multiclass
                   vv
clus                T1 T2 T3+T4
  7P GAIN MUTATED    3  5     5
  7P GAIN WILD-TYPE  1  2     3
D9V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                  3                 1
  T2                  5                 2
  T3+T4               5                 3
                   vv
clus                N0 N1+N2+N3
  7P GAIN MUTATED    3       10
  7P GAIN WILD-TYPE  4        2
D9V5, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                     3                 4
  N1+N2+N3              10                 2
D9V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    2 11
  7P GAIN WILD-TYPE  1  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   11
  7P GAIN WILD-TYPE    1    5
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               2                 1
  MALE                11                 5
D9V7, continuous

Clustering(10) Variable = 7Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2               0 1
  7Q GAIN MUTATED   8 1
  7Q GAIN WILD-TYPE 2 4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                 6 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                 4 
$`7Q GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         3.48         3.68         4.08         3.32         3.16 
TCGA-L5-A4OS TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71         0.13         0.07 

$`7Q GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        0.26        18.35         1.38        29.00         7.10         7.43 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.26 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            30.71             29.00 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            3.320             7.265 
[1] "0.0 - 30.7 (3.3)" "0.3 - 29.0 (7.3)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
[1] "hr=" "2.8"
D10V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  7Q GAIN MUTATED          2         2         4          0          1
  7Q GAIN WILD-TYPE        0         1         3          4          1
                   vv
clus                STAGE IIIC
  7Q GAIN MUTATED            1
  7Q GAIN WILD-TYPE          0
D10V3, multiclass
                   vv
clus                T1 T2 T3+T4
  7Q GAIN MUTATED    3  4     3
  7Q GAIN WILD-TYPE  1  3     5
D10V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                  3                 1
  T2                  4                 3
  T3+T4               3                 5
                   vv
clus                N0 N1+N2+N3
  7Q GAIN MUTATED    4        6
  7Q GAIN WILD-TYPE  3        6
D10V5, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                     4                 3
  N1+N2+N3               6                 6
D10V6, binary
                   cls
clus                0 1
  7Q GAIN MUTATED   2 8
  7Q GAIN WILD-TYPE 1 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    8
  7Q GAIN WILD-TYPE    1    8
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               2                 1
  MALE                 8                 8
D10V7, continuous

Clustering(11) Variable = 8P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2               0 1
  8P GAIN MUTATED   1 3
  8P GAIN WILD-TYPE 9 2
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                11 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                 2 
$`8P GAIN MUTATED`
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OW 
        4.08        18.35         3.16         7.10 

$`8P GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         0.26         3.48         3.68         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71        29.00         7.43         0.13         0.07 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             3.16              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            18.35             30.71 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             5.59              3.32 
[1] "3.2 - 18.4 (5.6)" "0.0 - 30.7 (3.3)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D11V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  8P GAIN MUTATED          2         0         3          1          0
  8P GAIN WILD-TYPE        0         3         4          3          2
                   vv
clus                STAGE IIIC
  8P GAIN MUTATED            0
  8P GAIN WILD-TYPE          1
D11V3, multiclass
                   vv
clus                T1 T2 T3+T4
  8P GAIN MUTATED    3  2     1
  8P GAIN WILD-TYPE  1  5     7
D11V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  3                 1
  T2                  2                 5
  T3+T4               1                 7
                   vv
clus                N0 N1+N2+N3
  8P GAIN MUTATED    3        3
  8P GAIN WILD-TYPE  4        9
D11V5, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                     3                 4
  N1+N2+N3               3                 9
D11V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    2  4
  8P GAIN WILD-TYPE  1 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    4
  8P GAIN WILD-TYPE    1   12
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               2                 1
  MALE                 4                12
D11V7, continuous

Clustering(12) Variable = 8Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2               0 1
  8Q GAIN MUTATED   4 4
  8Q GAIN WILD-TYPE 6 1
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                 7 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                 1 
$`8Q GAIN MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW 
        0.26         4.08        18.35         3.32         3.16         7.10 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

$`8Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        0.03         3.48         3.68         1.38        30.71        29.00 
TCGA-LN-A4A2 
        0.13 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.35             30.71 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             3.70              3.48 
[1] "0.1 - 18.4 (3.7)" "0.0 - 30.7 (3.5)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
[1] "hr=" "4"  
D12V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  8Q GAIN MUTATED          2         1         4          2          1
  8Q GAIN WILD-TYPE        0         2         3          2          1
                   vv
clus                STAGE IIIC
  8Q GAIN MUTATED            1
  8Q GAIN WILD-TYPE          0
D12V3, multiclass
                   vv
clus                T1 T2 T3+T4
  8Q GAIN MUTATED    3  4     4
  8Q GAIN WILD-TYPE  1  3     4
D12V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  3                 1
  T2                  4                 3
  T3+T4               4                 4
                   vv
clus                N0 N1+N2+N3
  8Q GAIN MUTATED    4        7
  8Q GAIN WILD-TYPE  3        5
D12V5, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                     4                 3
  N1+N2+N3               7                 5
D12V6, binary
                   cls
clus                0 1
  8Q GAIN MUTATED   2 9
  8Q GAIN WILD-TYPE 1 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    9
  8Q GAIN WILD-TYPE    1    7
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               2                 1
  MALE                 9                 7
D12V7, continuous

Clustering(13) Variable = 9Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2               0 1
  9Q GAIN MUTATED   3 0
  9Q GAIN WILD-TYPE 7 5
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                12 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 5 
$`9Q GAIN MUTATED`
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-LN-A4A9 
        3.32        29.00         0.07 

$`9Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38         3.16        30.71         7.10         7.43         0.13 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.07              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            29.00             30.71 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             3.32              3.58 
[1] "0.1 - 29.0 (3.3)" "0.0 - 30.7 (3.6)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
[1] "hr="     "7.7e+08"
D13V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  9Q GAIN MUTATED          0         2         0          0          0
  9Q GAIN WILD-TYPE        2         1         7          4          2
                   vv
clus                STAGE IIIC
  9Q GAIN MUTATED            1
  9Q GAIN WILD-TYPE          0
D13V3, multiclass
                   vv
clus                T1 T2 T3+T4
  9Q GAIN MUTATED    0  1     2
  9Q GAIN WILD-TYPE  4  6     6
D13V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1                  0                 4
  T2                  1                 6
  T3+T4               2                 6
                   vv
clus                N0 N1+N2+N3
  9Q GAIN MUTATED    2        1
  9Q GAIN WILD-TYPE  5       11
D13V5, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                     2                 5
  N1+N2+N3               1                11
D13V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0  3
  9Q GAIN WILD-TYPE  3 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE    3   13
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               0                 3
  MALE                 3                13
D13V7, continuous

Clustering(14) Variable = 11P GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                0 1
  11P GAIN MUTATED   4 1
  11P GAIN WILD-TYPE 6 4
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                  4 
$`11P GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OU 
        3.48         3.68         4.08         1.38        29.00 

$`11P GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         0.26        18.35         3.32         3.16        30.71 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         7.43         0.13         0.07 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.38               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             29.00              30.71 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              3.68               3.24 
[1] "1.4 - 29.0 (3.7)" "0.0 - 30.7 (3.2)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "11P GAIN MUTATED"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "11P GAIN MUTATED"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "11P GAIN MUTATED"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D14V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  11P GAIN MUTATED          1         1         1          1          1
  11P GAIN WILD-TYPE        1         2         6          3          1
                    vv
clus                 STAGE IIIC
  11P GAIN MUTATED            0
  11P GAIN WILD-TYPE          1
D14V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  11P GAIN MUTATED    2  1     2
  11P GAIN WILD-TYPE  2  6     6
D14V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   2                  2
  T2                   1                  6
  T3+T4                2                  6
                    vv
clus                 N0 N1+N2+N3
  11P GAIN MUTATED    2        3
  11P GAIN WILD-TYPE  5        9
D14V5, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                      2                  5
  N1+N2+N3                3                  9
D14V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  4
  11P GAIN WILD-TYPE  2 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    4
  11P GAIN WILD-TYPE    2   12
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                1                  2
  MALE                  4                 12
D14V7, continuous

Clustering(15) Variable = 11Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                0 1
  11Q GAIN MUTATED   2 1
  11Q GAIN WILD-TYPE 8 4
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 12 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                  4 
$`11Q GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OQ 
        3.48         3.68         1.38 

$`11Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         0.26         4.08        18.35         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71        29.00         7.10         7.43         0.13         0.07 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.38               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              3.68              30.71 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              3.48               3.70 
[1] "1.4 - 3.7 (3.5)"  "0.0 - 30.7 (3.7)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "3.3"
D15V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED          0         0         1          1          1
  11Q GAIN WILD-TYPE        2         3         6          3          1
                    vv
clus                 STAGE IIIC
  11Q GAIN MUTATED            0
  11Q GAIN WILD-TYPE          1
D15V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  11Q GAIN MUTATED    1  1     1
  11Q GAIN WILD-TYPE  3  6     7
D15V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                1                  7
                    vv
clus                 N0 N1+N2+N3
  11Q GAIN MUTATED    0        3
  11Q GAIN WILD-TYPE  7        9
D15V5, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                      0                  7
  N1+N2+N3                3                  9
D15V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    0  3
  11Q GAIN WILD-TYPE  3 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    3
  11Q GAIN WILD-TYPE    3   13
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                0                  3
  MALE                  3                 13
D15V7, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 10 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A4P3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-LN-A4A9 
"11Q GAIN WILD-TYPE" 

Clustering(16) Variable = 12P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                0 1
  12P GAIN MUTATED   4 0
  12P GAIN WILD-TYPE 6 5
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 11 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  5 
$`12P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OO 
        0.03         3.48         4.08         3.32 

$`12P GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.26         3.68        18.35         1.38         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         7.10         7.43         0.13         0.07 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.03               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              4.08              30.71 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              3.40               3.68 
[1] "0.0 - 4.1 (3.4)"  "0.1 - 30.7 (3.7)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr="     "3.1e+08"
D16V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  12P GAIN MUTATED          1         0         1          1          1
  12P GAIN WILD-TYPE        1         3         6          3          1
                    vv
clus                 STAGE IIIC
  12P GAIN MUTATED            1
  12P GAIN WILD-TYPE          0
D16V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  12P GAIN MUTATED    1  1     3
  12P GAIN WILD-TYPE  3  6     5
D16V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  12P GAIN MUTATED    1        4
  12P GAIN WILD-TYPE  6        8
D16V5, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                      1                  6
  N1+N2+N3                4                  8
D16V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  4
  12P GAIN WILD-TYPE  2 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    4
  12P GAIN WILD-TYPE    2   12
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                1                  2
  MALE                  4                 12
D16V7, continuous

Clustering(17) Variable = 12Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                0 1
  12Q GAIN MUTATED   5 0
  12Q GAIN WILD-TYPE 5 5
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  5 
$`12Q GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OO TCGA-LN-A4A9 
        0.03         3.48         4.08         3.32         0.07 

$`12Q GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.26         3.68        18.35         1.38         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
       29.00         7.10         7.43         0.13 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.03               0.13 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              4.08              30.71 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              3.32               5.39 
[1] "0.0 - 4.1 (3.3)"  "0.1 - 30.7 (5.4)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
[1] "hr="     "3.1e+08"
D17V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED          1         1         1          1          1
  12Q GAIN WILD-TYPE        1         2         6          3          1
                    vv
clus                 STAGE IIIC
  12Q GAIN MUTATED            1
  12Q GAIN WILD-TYPE          0
D17V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  12Q GAIN MUTATED    1  2     3
  12Q GAIN WILD-TYPE  3  5     5
D17V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                   1                  3
  T2                   2                  5
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  12Q GAIN MUTATED    2        4
  12Q GAIN WILD-TYPE  5        8
D17V5, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                      2                  5
  N1+N2+N3                4                  8
D17V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  5
  12Q GAIN WILD-TYPE  2 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    5
  12Q GAIN WILD-TYPE    2   11
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                  2
  MALE                  5                 11
D17V7, continuous

Clustering(18) Variable = 14Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                0 1
  14Q GAIN MUTATED   2 1
  14Q GAIN WILD-TYPE 8 4
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 12 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  4 
$`14Q GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OR TCGA-LN-A4A9 
        0.03         3.16         0.07 

$`14Q GAIN WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.48         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38        30.71        29.00         7.10         7.43         0.13 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.03               0.13 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.16              30.71 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.07               3.88 
[1] "0.0 - 3.2 (0.1)"  "0.1 - 30.7 (3.9)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
[1] "hr=" "9.5"
D18V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED          1         1         1          2          0
  14Q GAIN WILD-TYPE        1         2         6          2          2
                    vv
clus                 STAGE IIIC
  14Q GAIN MUTATED            0
  14Q GAIN WILD-TYPE          1
D18V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  14Q GAIN MUTATED    1  2     2
  14Q GAIN WILD-TYPE  3  5     6
D18V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   1                  3
  T2                   2                  5
  T3+T4                2                  6
                    vv
clus                 N0 N1+N2+N3
  14Q GAIN MUTATED    4        1
  14Q GAIN WILD-TYPE  3       11
D18V5, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                      4                  3
  N1+N2+N3                1                 11
D18V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    0  5
  14Q GAIN WILD-TYPE  3 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    5
  14Q GAIN WILD-TYPE    3   11
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                0                  3
  MALE                  5                 11
D18V7, continuous

Clustering(19) Variable = 16P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                0 1
  16P GAIN MUTATED   3 0
  16P GAIN WILD-TYPE 7 5
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 12 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  5 
$`16P GAIN MUTATED`
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-LN-A4A9 
        3.32        29.00         0.07 

$`16P GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38         3.16        30.71         7.10         7.43         0.13 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             29.00              30.71 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.32               3.58 
[1] "0.1 - 29.0 (3.3)" "0.0 - 30.7 (3.6)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
[1] "hr="     "7.7e+08"
D19V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  16P GAIN MUTATED          0         2         0          1          0
  16P GAIN WILD-TYPE        2         1         7          3          2
                    vv
clus                 STAGE IIIC
  16P GAIN MUTATED            1
  16P GAIN WILD-TYPE          0
D19V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  16P GAIN MUTATED    0  1     3
  16P GAIN WILD-TYPE  4  6     5
D19V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                   0                  4
  T2                   1                  6
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  16P GAIN MUTATED    3        1
  16P GAIN WILD-TYPE  4       11
D19V5, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                      3                  4
  N1+N2+N3                1                 11
D19V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    0  4
  16P GAIN WILD-TYPE  3 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0    4
  16P GAIN WILD-TYPE    3   12
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                0                  3
  MALE                  4                 12
D19V7, continuous

Clustering(20) Variable = 16Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                0 1
  16Q GAIN MUTATED   3 0
  16Q GAIN WILD-TYPE 7 5
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 12 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 0                  5 
$`16Q GAIN MUTATED`
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-LN-A4A9 
        3.32        29.00         0.07 

$`16Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38         3.16        30.71         7.10         7.43         0.13 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.07               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             29.00              30.71 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.32               3.58 
[1] "0.1 - 29.0 (3.3)" "0.0 - 30.7 (3.6)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
[1] "hr="     "7.7e+08"
D20V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED          0         2         0          1          0
  16Q GAIN WILD-TYPE        2         1         7          3          2
                    vv
clus                 STAGE IIIC
  16Q GAIN MUTATED            1
  16Q GAIN WILD-TYPE          0
D20V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  16Q GAIN MUTATED    0  1     3
  16Q GAIN WILD-TYPE  4  6     5
D20V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                   0                  4
  T2                   1                  6
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  16Q GAIN MUTATED    3        1
  16Q GAIN WILD-TYPE  4       11
D20V5, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                      3                  4
  N1+N2+N3                1                 11
D20V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    0  4
  16Q GAIN WILD-TYPE  3 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    4
  16Q GAIN WILD-TYPE    3   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                0                  3
  MALE                  4                 12
D20V7, continuous

Clustering(21) Variable = 17Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                0 1
  17Q GAIN MUTATED   3 1
  17Q GAIN WILD-TYPE 7 4
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 11 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                  4 
$`17Q GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-LN-A4A2 
        3.48         3.32         1.38         0.13 

$`17Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR 
        0.03         0.26         3.68         4.08        18.35         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
       30.71        29.00         7.10         7.43         0.07 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.13               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              3.48              30.71 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2.35               4.08 
[1] "0.1 - 3.5 (2.3)"  "0.0 - 30.7 (4.1)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
[1] "hr=" "3.3"
D21V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED          0         1         1          1          1
  17Q GAIN WILD-TYPE        2         2         6          3          1
                    vv
clus                 STAGE IIIC
  17Q GAIN MUTATED            1
  17Q GAIN WILD-TYPE          0
D21V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  17Q GAIN MUTATED    0  2     3
  17Q GAIN WILD-TYPE  4  5     5
D21V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                   0                  4
  T2                   2                  5
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  17Q GAIN MUTATED    1        4
  17Q GAIN WILD-TYPE  6        8
D21V5, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                      1                  6
  N1+N2+N3                4                  8
D21V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  5
  17Q GAIN WILD-TYPE  3 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    5
  17Q GAIN WILD-TYPE    3   11
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                0                  3
  MALE                  5                 11
D21V7, continuous

Clustering(22) Variable = 18P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                0 1
  18P GAIN MUTATED   1 4
  18P GAIN WILD-TYPE 9 1
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                  1 
$`18P GAIN MUTATED`
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW 
        4.08        18.35         1.38         3.16         7.10 

$`18P GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OS 
        0.03         0.26         3.48         3.68         3.32        30.71 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         7.43         0.13         0.07 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.38               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             18.35              30.71 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              4.08               3.40 
[1] "1.4 - 18.4 (4.1)" "0.0 - 30.7 (3.4)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "7.2"
D22V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  18P GAIN MUTATED          2         0         2          1          0
  18P GAIN WILD-TYPE        0         3         5          3          2
                    vv
clus                 STAGE IIIC
  18P GAIN MUTATED            0
  18P GAIN WILD-TYPE          1
D22V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  18P GAIN MUTATED    3  2     0
  18P GAIN WILD-TYPE  1  5     8
D22V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   3                  1
  T2                   2                  5
  T3+T4                0                  8
                    vv
clus                 N0 N1+N2+N3
  18P GAIN MUTATED    2        3
  18P GAIN WILD-TYPE  5        9
D22V5, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                      2                  5
  N1+N2+N3                3                  9
D22V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  3
  18P GAIN WILD-TYPE  1 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    3
  18P GAIN WILD-TYPE    1   13
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                  1
  MALE                  3                 13
D22V7, continuous

Clustering(23) Variable = 19P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                0 1
  19P GAIN MUTATED   2 2
  19P GAIN WILD-TYPE 8 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 11 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                  3 
$`19P GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        3.48         3.32         1.38         3.16 

$`19P GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OS 
        0.03         0.26         3.68         4.08        18.35        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         7.10         7.43         0.13         0.07 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.38               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              3.48              30.71 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              3.24               4.08 
[1] "1.4 - 3.5 (3.2)"  "0.0 - 30.7 (4.1)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "19P GAIN MUTATED"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "19P GAIN MUTATED"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "19P GAIN MUTATED"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr="     "1.6e+09"
D23V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  19P GAIN MUTATED          1         0         0          1          1
  19P GAIN WILD-TYPE        1         3         7          3          1
                    vv
clus                 STAGE IIIC
  19P GAIN MUTATED            1
  19P GAIN WILD-TYPE          0
D23V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  19P GAIN MUTATED    1  1     2
  19P GAIN WILD-TYPE  3  6     6
D23V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                2                  6
                    vv
clus                 N0 N1+N2+N3
  19P GAIN MUTATED    1        3
  19P GAIN WILD-TYPE  6        9
D23V5, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                      1                  6
  N1+N2+N3                3                  9
D23V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0  4
  19P GAIN WILD-TYPE  3 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    4
  19P GAIN WILD-TYPE    3   12
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                0                  3
  MALE                  4                 12
D23V7, continuous

Clustering(24) Variable = 19Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                0 1
  19Q GAIN MUTATED   4 2
  19Q GAIN WILD-TYPE 6 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                  9 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  3 
$`19Q GAIN MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.26         3.48         3.68         3.32         1.38         3.16 

$`19Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        0.03         4.08        18.35        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.43         0.13         0.07 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.26               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              3.68              30.71 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              3.24               7.10 
[1] "0.3 - 3.7 (3.2)"  "0.0 - 30.7 (7.1)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr="     "8.4e+08"
D24V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED          1         0         1          1          2
  19Q GAIN WILD-TYPE        1         3         6          3          0
                    vv
clus                 STAGE IIIC
  19Q GAIN MUTATED            1
  19Q GAIN WILD-TYPE          0
D24V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  19Q GAIN MUTATED    2  1     3
  19Q GAIN WILD-TYPE  2  6     5
D24V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   2                  2
  T2                   1                  6
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  19Q GAIN MUTATED    1        5
  19Q GAIN WILD-TYPE  6        7
D24V5, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                      1                  6
  N1+N2+N3                5                  7
D24V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    0  6
  19Q GAIN WILD-TYPE  3 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    6
  19Q GAIN WILD-TYPE    3   10
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                0                  3
  MALE                  6                 10
D24V7, continuous

Clustering(25) Variable = 20P GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                0 1
  20P GAIN MUTATED   8 4
  20P GAIN WILD-TYPE 2 1
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                  3 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 4                  1 
$`20P GAIN MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         4.08        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71        29.00         7.10         7.43         0.13         0.07 

$`20P GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OR 
        0.03         3.68         3.16 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             30.71               3.68 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              3.78               3.16 
[1] "0.1 - 30.7 (3.8)" "0.0 - 3.7 (3.2)" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
[1] "hr=" "4.2"
D25V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  20P GAIN MUTATED          1         3         5          3          2
  20P GAIN WILD-TYPE        1         0         2          1          0
                    vv
clus                 STAGE IIIC
  20P GAIN MUTATED            1
  20P GAIN WILD-TYPE          0
D25V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  20P GAIN MUTATED    2  6     7
  20P GAIN WILD-TYPE  2  1     1
D25V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                   2                  2
  T2                   6                  1
  T3+T4                7                  1
                    vv
clus                 N0 N1+N2+N3
  20P GAIN MUTATED    5       10
  20P GAIN WILD-TYPE  2        2
D25V5, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                      5                  2
  N1+N2+N3               10                  2
D25V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    3 12
  20P GAIN WILD-TYPE  0  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   12
  20P GAIN WILD-TYPE    0    4
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                3                  0
  MALE                 12                  4
D25V7, continuous
[1] "Remove cluster labels:" "20P GAIN WILD-TYPE"    
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                  2 
      TCGA-IG-A3Y9       TCGA-L5-A4OE       TCGA-L5-A4OM       TCGA-L5-A4ON 
"20P GAIN MUTATED" "20P GAIN MUTATED" "20P GAIN MUTATED" "20P GAIN MUTATED" 
      TCGA-L5-A4OO       TCGA-L5-A4OQ       TCGA-L5-A4OU       TCGA-L5-A4OW 
"20P GAIN MUTATED" "20P GAIN MUTATED" "20P GAIN MUTATED" "20P GAIN MUTATED" 
      TCGA-L5-A4OX       TCGA-LN-A4A9 
"20P GAIN MUTATED" "20P GAIN MUTATED" 

Clustering(26) Variable = 20Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                0 1
  20Q GAIN MUTATED   8 5
  20Q GAIN WILD-TYPE 2 0
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                  2 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                  0 
$`20Q GAIN MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.48         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        30.71        29.00         7.10         7.43 
TCGA-LN-A4A2 
        0.13 

$`20Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-LN-A4A9 
        0.03         0.07 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.13               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             30.71               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              3.68               0.05 
[1] "0.1 - 30.7 (3.7)" "0.0 - 0.1 (0.1)" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "20Q GAIN WILD-TYPE"    
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                  2 
      TCGA-IG-A4QS       TCGA-L5-A4OE       TCGA-L5-A4OF       TCGA-L5-A4OM 
"20Q GAIN MUTATED" "20Q GAIN MUTATED" "20Q GAIN MUTATED" "20Q GAIN MUTATED" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OQ       TCGA-L5-A4OR 
"20Q GAIN MUTATED" "20Q GAIN MUTATED" "20Q GAIN MUTATED" "20Q GAIN MUTATED" 
      TCGA-L5-A4OS       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"20Q GAIN MUTATED" "20Q GAIN MUTATED" "20Q GAIN MUTATED" "20Q GAIN MUTATED" 
      TCGA-LN-A4A2 
"20Q GAIN MUTATED" 
D26V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED          2         2         6          3          2
  20Q GAIN WILD-TYPE        0         1         1          1          0
                    vv
clus                 STAGE IIIC
  20Q GAIN MUTATED            1
  20Q GAIN WILD-TYPE          0
D26V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  20Q GAIN MUTATED    4  5     7
  20Q GAIN WILD-TYPE  0  2     1
D26V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                   4                  0
  T2                   5                  2
  T3+T4                7                  1
                    vv
clus                 N0 N1+N2+N3
  20Q GAIN MUTATED    5       11
  20Q GAIN WILD-TYPE  2        1
D26V5, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                      5                  2
  N1+N2+N3               11                  1
D26V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    3 13
  20Q GAIN WILD-TYPE  0  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   13
  20Q GAIN WILD-TYPE    0    3
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                3                  0
  MALE                 13                  3
D26V7, continuous

Clustering(27) Variable = 22Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                0 1
  22Q GAIN MUTATED   3 0
  22Q GAIN WILD-TYPE 7 5
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 12 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  5 
$`22Q GAIN MUTATED`
TCGA-L5-A4OM TCGA-LN-A4A2 TCGA-LN-A4A9 
        4.08         0.13         0.07 

$`22Q GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.48         3.68        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        30.71        29.00         7.10         7.43 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              4.08              30.71 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               3.58 
[1] "0.1 - 4.1 (0.1)"  "0.0 - 30.7 (3.6)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
[1] "hr="     "7.7e+07"
D27V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED          1         2         0          2          0
  22Q GAIN WILD-TYPE        1         1         7          2          2
                    vv
clus                 STAGE IIIC
  22Q GAIN MUTATED            0
  22Q GAIN WILD-TYPE          1
D27V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  22Q GAIN MUTATED    1  1     3
  22Q GAIN WILD-TYPE  3  6     5
D27V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  22Q GAIN MUTATED    5        0
  22Q GAIN WILD-TYPE  2       12
D27V5, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                      5                  2
  N1+N2+N3                0                 12
D27V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1  4
  22Q GAIN WILD-TYPE  2 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    4
  22Q GAIN WILD-TYPE    2   12
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                1                  2
  MALE                  4                 12
D27V7, continuous

Clustering(28) Variable = XQ GAIN MUTATION ANALYSIS
D28V1, survival
                   sevent
clus2               0 1
  XQ GAIN MUTATED   4 1
  XQ GAIN WILD-TYPE 6 4
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5                10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 4 
$`XQ GAIN MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OQ TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.26         3.48         1.38         0.13         0.07 

$`XQ GAIN WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         3.68         4.08        18.35         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       30.71        29.00         7.10         7.43 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3.48             30.71 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.26              5.59 
[1] "0.1 - 3.5 (0.3)"  "0.0 - 30.7 (5.6)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
[1] "hr=" "6.4"
D28V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  XQ GAIN MUTATED          0         2         1          1          2
  XQ GAIN WILD-TYPE        2         1         6          3          0
                   vv
clus                STAGE IIIC
  XQ GAIN MUTATED            0
  XQ GAIN WILD-TYPE          1
D28V3, multiclass
                   vv
clus                T1 T2 T3+T4
  XQ GAIN MUTATED    0  3     3
  XQ GAIN WILD-TYPE  4  4     5
D28V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                  0                 4
  T2                  3                 4
  T3+T4               3                 5
                   vv
clus                N0 N1+N2+N3
  XQ GAIN MUTATED    2        4
  XQ GAIN WILD-TYPE  5        8
D28V5, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                     2                 5
  N1+N2+N3               4                 8
D28V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0  6
  XQ GAIN WILD-TYPE  3 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    6
  XQ GAIN WILD-TYPE    3   10
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               0                 3
  MALE                 6                10
D28V7, continuous

Clustering(29) Variable = 3P LOSS MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2               0 1
  3P LOSS MUTATED   3 2
  3P LOSS WILD-TYPE 7 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 3 
$`3P LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OO TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        0.26         3.32         7.10         7.43         0.13 

$`3P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.03         3.48         3.68         4.08        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-LN-A4A9 
        3.16        30.71        29.00         0.07 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             7.43             30.71 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             3.32              3.58 
[1] "0.1 - 7.4 (3.3)"  "0.0 - 30.7 (3.6)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D29V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  3P LOSS MUTATED          0         1         3          3          1
  3P LOSS WILD-TYPE        2         2         4          1          1
                   vv
clus                STAGE IIIC
  3P LOSS MUTATED            1
  3P LOSS WILD-TYPE          0
D29V3, multiclass
                   vv
clus                T1 T2 T3+T4
  3P LOSS MUTATED    0  3     6
  3P LOSS WILD-TYPE  4  4     2
D29V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  0                 4
  T2                  3                 4
  T3+T4               6                 2
                   vv
clus                N0 N1+N2+N3
  3P LOSS MUTATED    3        6
  3P LOSS WILD-TYPE  4        6
D29V5, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                     3                 4
  N1+N2+N3               6                 6
D29V6, binary
                   cls
clus                0 1
  3P LOSS MUTATED   1 8
  3P LOSS WILD-TYPE 2 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    8
  3P LOSS WILD-TYPE    2    8
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               1                 2
  MALE                 8                 8
D29V7, continuous

Clustering(30) Variable = 4P LOSS MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2               0 1
  4P LOSS MUTATED   5 3
  4P LOSS WILD-TYPE 5 2
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                 7 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                 2 
$`4P LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW 
        0.03         0.26         3.48         3.32         3.16         7.10 
TCGA-L5-A4OX TCGA-LN-A4A2 
        7.43         0.13 

$`4P LOSS WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        3.68         4.08        18.35         1.38        30.71        29.00 
TCGA-LN-A4A9 
        0.07 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             7.43             30.71 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             3.24              4.08 
[1] "0.0 - 7.4 (3.2)"  "0.1 - 30.7 (4.1)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
[1] "hr=" "4.8"
D30V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  4P LOSS MUTATED          1         1         3          2          2
  4P LOSS WILD-TYPE        1         2         4          2          0
                   vv
clus                STAGE IIIC
  4P LOSS MUTATED            1
  4P LOSS WILD-TYPE          0
D30V3, multiclass
                   vv
clus                T1 T2 T3+T4
  4P LOSS MUTATED    1  3     6
  4P LOSS WILD-TYPE  3  4     2
D30V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  1                 3
  T2                  3                 4
  T3+T4               6                 2
                   vv
clus                N0 N1+N2+N3
  4P LOSS MUTATED    4        6
  4P LOSS WILD-TYPE  3        6
D30V5, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                     4                 3
  N1+N2+N3               6                 6
D30V6, binary
                   cls
clus                0 1
  4P LOSS MUTATED   1 9
  4P LOSS WILD-TYPE 2 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    9
  4P LOSS WILD-TYPE    2    7
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               1                 2
  MALE                 9                 7
D30V7, continuous

Clustering(31) Variable = 4Q LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2               0 1
  4Q LOSS MUTATED   3 3
  4Q LOSS WILD-TYPE 7 2
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                 9 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                 2 
$`4Q LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX 
        0.26         3.48         3.32         3.16         7.10         7.43 

$`4Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.03         3.68         4.08        18.35         1.38        30.71 
TCGA-L5-A4OU TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         0.13         0.07 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.26              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             7.43             30.71 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             3.40              3.68 
[1] "0.3 - 7.4 (3.4)"  "0.0 - 30.7 (3.7)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "4.8"
D31V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  4Q LOSS MUTATED          1         0         2          1          2
  4Q LOSS WILD-TYPE        1         3         5          3          0
                   vv
clus                STAGE IIIC
  4Q LOSS MUTATED            1
  4Q LOSS WILD-TYPE          0
D31V3, multiclass
                   vv
clus                T1 T2 T3+T4
  4Q LOSS MUTATED    1  2     4
  4Q LOSS WILD-TYPE  3  5     4
D31V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  1                 3
  T2                  2                 5
  T3+T4               4                 4
                   vv
clus                N0 N1+N2+N3
  4Q LOSS MUTATED    2        5
  4Q LOSS WILD-TYPE  5        7
D31V5, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                     2                 5
  N1+N2+N3               5                 7
D31V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  6
  4Q LOSS WILD-TYPE  2 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    6
  4Q LOSS WILD-TYPE    2   10
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               1                 2
  MALE                 6                10
D31V7, continuous

Clustering(32) Variable = 5P LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2               0 1
  5P LOSS MUTATED   4 0
  5P LOSS WILD-TYPE 6 5
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                11 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                 5 
$`5P LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OS 
        0.26         3.48         3.68        30.71 

$`5P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.03         4.08        18.35         3.32         1.38         3.16 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         7.10         7.43         0.13         0.07 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.26              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            30.71             29.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.58              3.32 
[1] "0.3 - 30.7 (3.6)" "0.0 - 29.0 (3.3)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED"   "5P LOSS MUTATED"   "5P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED"   "5P LOSS MUTATED"   "5P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED"   "5P LOSS MUTATED"   "5P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr="     "8.3e+08"
D32V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  5P LOSS MUTATED          0         0         3          0          2
  5P LOSS WILD-TYPE        2         3         4          4          0
                   vv
clus                STAGE IIIC
  5P LOSS MUTATED            0
  5P LOSS WILD-TYPE          1
D32V3, multiclass
                   vv
clus                T1 T2 T3+T4
  5P LOSS MUTATED    1  2     2
  5P LOSS WILD-TYPE  3  5     6
D32V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  1                 3
  T2                  2                 5
  T3+T4               2                 6
                   vv
clus                N0 N1+N2+N3
  5P LOSS MUTATED    0        5
  5P LOSS WILD-TYPE  7        7
D32V5, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                     0                 7
  N1+N2+N3               5                 7
D32V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  4
  5P LOSS WILD-TYPE  2 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    4
  5P LOSS WILD-TYPE    2   12
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               1                 2
  MALE                 4                12
D32V7, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                11 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A4P3        TCGA-L5-A4OM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ        TCGA-L5-A4OU 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-LN-A4A9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 

Clustering(33) Variable = 5Q LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2               0 1
  5Q LOSS MUTATED   7 2
  5Q LOSS WILD-TYPE 3 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                 6 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 3 
$`5Q LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR 
        0.03         0.26         3.48         3.68         4.08         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
       30.71         7.10         0.13 

$`5Q LOSS WILD-TYPE`
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
       18.35         3.32         1.38        29.00         7.43         0.07 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.03              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            30.71             29.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            3.480             5.375 
[1] "0.0 - 30.7 (3.5)" "0.1 - 29.0 (5.4)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D33V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  5Q LOSS MUTATED          2         1         4          1          2
  5Q LOSS WILD-TYPE        0         2         3          3          0
                   vv
clus                STAGE IIIC
  5Q LOSS MUTATED            0
  5Q LOSS WILD-TYPE          1
D33V3, multiclass
                   vv
clus                T1 T2 T3+T4
  5Q LOSS MUTATED    3  3     4
  5Q LOSS WILD-TYPE  1  4     4
D33V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  3                 1
  T2                  3                 4
  T3+T4               4                 4
                   vv
clus                N0 N1+N2+N3
  5Q LOSS MUTATED    3        7
  5Q LOSS WILD-TYPE  4        5
D33V5, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                     3                 4
  N1+N2+N3               7                 5
D33V6, binary
                   cls
clus                0 1
  5Q LOSS MUTATED   3 7
  5Q LOSS WILD-TYPE 0 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    7
  5Q LOSS WILD-TYPE    0    9
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3                 0
  MALE                 7                 9
D33V7, continuous

Clustering(34) Variable = 8P LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2               0 1
  8P LOSS MUTATED   5 1
  8P LOSS WILD-TYPE 5 4
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                 9 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 4 
$`8P LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OX TCGA-LN-A4A2 
        0.26         3.48         3.68         3.32         7.43         0.13 

$`8P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         4.08        18.35         1.38         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
       29.00         7.10         0.07 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.13              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             7.43             30.71 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3.40              4.08 
[1] "0.1 - 7.4 (3.4)"  "0.0 - 30.7 (4.1)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D34V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  8P LOSS MUTATED          0         1         2          2          2
  8P LOSS WILD-TYPE        2         2         5          2          0
                   vv
clus                STAGE IIIC
  8P LOSS MUTATED            1
  8P LOSS WILD-TYPE          0
D34V3, multiclass
                   vv
clus                T1 T2 T3+T4
  8P LOSS MUTATED    1  1     6
  8P LOSS WILD-TYPE  3  6     2
D34V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  1                 3
  T2                  1                 6
  T3+T4               6                 2
                   vv
clus                N0 N1+N2+N3
  8P LOSS MUTATED    2        6
  8P LOSS WILD-TYPE  5        6
D34V5, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                     2                 5
  N1+N2+N3               6                 6
D34V6, binary
                   cls
clus                0 1
  8P LOSS MUTATED   0 8
  8P LOSS WILD-TYPE 3 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    8
  8P LOSS WILD-TYPE    3    8
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               0                 3
  MALE                 8                 8
D34V7, continuous

Clustering(35) Variable = 9P LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2               0 1
  9P LOSS MUTATED   7 2
  9P LOSS WILD-TYPE 3 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                 6 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 3 
$`9P LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.68         4.08        18.35         3.32 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
       30.71         7.10         0.13 

$`9P LOSS WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
        3.48         1.38         3.16        29.00         7.43         0.07 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            30.71             29.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             3.68              3.32 
[1] "0.0 - 30.7 (3.7)" "0.1 - 29.0 (3.3)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D35V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  9P LOSS MUTATED          1         1         5          1          1
  9P LOSS WILD-TYPE        1         2         2          3          1
                   vv
clus                STAGE IIIC
  9P LOSS MUTATED            1
  9P LOSS WILD-TYPE          0
D35V3, multiclass
                   vv
clus                T1 T2 T3+T4
  9P LOSS MUTATED    3  3     4
  9P LOSS WILD-TYPE  1  4     4
D35V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  3                 1
  T2                  3                 4
  T3+T4               4                 4
                   vv
clus                N0 N1+N2+N3
  9P LOSS MUTATED    3        7
  9P LOSS WILD-TYPE  4        5
D35V5, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                     3                 4
  N1+N2+N3               7                 5
D35V6, binary
                   cls
clus                0 1
  9P LOSS MUTATED   3 7
  9P LOSS WILD-TYPE 0 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3    7
  9P LOSS WILD-TYPE    0    9
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               3                 0
  MALE                 7                 9
D35V7, continuous

Clustering(36) Variable = 9Q LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2               0 1
  9Q LOSS MUTATED   6 1
  9Q LOSS WILD-TYPE 4 4
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                 8 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 4 
$`9Q LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OW 
        0.03         0.26         3.68         4.08        30.71         7.10 
TCGA-LN-A4A2 
        0.13 

$`9Q LOSS WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU 
        3.48        18.35         3.32         1.38         3.16        29.00 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            30.71             29.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             3.68              3.40 
[1] "0.0 - 30.7 (3.7)" "0.1 - 29.0 (3.4)"
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-L5-A4OE        TCGA-L5-A4OF 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OU        TCGA-L5-A4OW 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-L5-A4OX        TCGA-LN-A4A2        TCGA-LN-A4A9 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D36V2, continuous
                   vv
clus                STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  9Q LOSS MUTATED          1         1         4          2          1
  9Q LOSS WILD-TYPE        1         2         3          2          1
                   vv
clus                STAGE IIIC
  9Q LOSS MUTATED            0
  9Q LOSS WILD-TYPE          1
D36V3, multiclass
                   vv
clus                T1 T2 T3+T4
  9Q LOSS MUTATED    2  3     4
  9Q LOSS WILD-TYPE  2  4     4
D36V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  2                 2
  T2                  3                 4
  T3+T4               4                 4
                   vv
clus                N0 N1+N2+N3
  9Q LOSS MUTATED    4        5
  9Q LOSS WILD-TYPE  3        7
D36V5, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                     4                 3
  N1+N2+N3               5                 7
D36V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    3  6
  9Q LOSS WILD-TYPE  0 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    6
  9Q LOSS WILD-TYPE    0   10
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               3                 0
  MALE                 6                10
D36V7, continuous

Clustering(37) Variable = 10P LOSS MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                0 1
  10P LOSS MUTATED   3 1
  10P LOSS WILD-TYPE 7 4
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 11 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                  4 
$`10P LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OW TCGA-LN-A4A9 
        3.48         3.32         7.10         0.07 

$`10P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.03         0.26         3.68         4.08        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 
        3.16        30.71        29.00         7.43         0.13 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              7.10              30.71 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              3.40               3.68 
[1] "0.1 - 7.1 (3.4)"  "0.0 - 30.7 (3.7)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
[1] "hr=" "1.4"
D37V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  10P LOSS MUTATED          0         1         1          1          1
  10P LOSS WILD-TYPE        2         2         6          3          1
                    vv
clus                 STAGE IIIC
  10P LOSS MUTATED            1
  10P LOSS WILD-TYPE          0
D37V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  10P LOSS MUTATED    0  2     3
  10P LOSS WILD-TYPE  4  5     5
D37V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                   0                  4
  T2                   2                  5
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  10P LOSS MUTATED    2        3
  10P LOSS WILD-TYPE  5        9
D37V5, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                      2                  5
  N1+N2+N3                3                  9
D37V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  4
  10P LOSS WILD-TYPE  2 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    4
  10P LOSS WILD-TYPE    2   12
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  4                 12
D37V7, continuous

Clustering(38) Variable = 10Q LOSS MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                0 1
  10Q LOSS MUTATED   3 1
  10Q LOSS WILD-TYPE 7 4
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 4                 11 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  4 
$`10Q LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OW TCGA-LN-A4A2 
        3.48         3.32         7.10         0.13 

$`10Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.03         0.26         3.68         4.08        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
        3.16        30.71        29.00         7.43         0.07 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.13               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              7.10              30.71 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              3.40               3.68 
[1] "0.1 - 7.1 (3.4)"  "0.0 - 30.7 (3.7)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D38V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED          0         1         1          2          1
  10Q LOSS WILD-TYPE        2         2         6          2          1
                    vv
clus                 STAGE IIIC
  10Q LOSS MUTATED            1
  10Q LOSS WILD-TYPE          0
D38V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  10Q LOSS MUTATED    0  1     5
  10Q LOSS WILD-TYPE  4  6     3
D38V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   0                  4
  T2                   1                  6
  T3+T4                5                  3
                    vv
clus                 N0 N1+N2+N3
  10Q LOSS MUTATED    2        4
  10Q LOSS WILD-TYPE  5        8
D38V5, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                      2                  5
  N1+N2+N3                4                  8
D38V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    1  5
  10Q LOSS WILD-TYPE  2 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    5
  10Q LOSS WILD-TYPE    2   11
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  5                 11
D38V7, continuous

Clustering(39) Variable = 11P LOSS MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                0 1
  11P LOSS MUTATED   2 1
  11P LOSS WILD-TYPE 8 4
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 12 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  4 
$`11P LOSS MUTATED`
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-LN-A4A2 
        3.32         3.16         0.13 

$`11P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        1.38        30.71        29.00         7.10         7.43         0.07 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.13               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              3.32              30.71 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              3.16               3.88 
[1] "0.1 - 3.3 (3.2)"  "0.0 - 30.7 (3.9)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
[1] "hr=" "4.2"
D39V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  11P LOSS MUTATED          1         1         0          2          0
  11P LOSS WILD-TYPE        1         2         7          2          2
                    vv
clus                 STAGE IIIC
  11P LOSS MUTATED            1
  11P LOSS WILD-TYPE          0
D39V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  11P LOSS MUTATED    1  0     4
  11P LOSS WILD-TYPE  3  7     4
D39V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   1                  3
  T2                   0                  7
  T3+T4                4                  4
                    vv
clus                 N0 N1+N2+N3
  11P LOSS MUTATED    3        2
  11P LOSS WILD-TYPE  4       10
D39V5, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                      3                  4
  N1+N2+N3                2                 10
D39V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    0  5
  11P LOSS WILD-TYPE  3 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    5
  11P LOSS WILD-TYPE    3   11
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                0                  3
  MALE                  5                 11
D39V7, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 10 
        TCGA-IG-A3YA         TCGA-IG-A4P3         TCGA-L5-A4OE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OQ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-LN-A4A9 
"11P LOSS WILD-TYPE" 

Clustering(40) Variable = 11Q LOSS MUTATION ANALYSIS
D40V1, survival
                    sevent
clus2                0 1
  11Q LOSS MUTATED   5 1
  11Q LOSS WILD-TYPE 5 4
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                  9 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  4 
$`11Q LOSS MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OU TCGA-LN-A4A2 
        0.03         4.08         3.32         3.16        29.00         0.13 

$`11Q LOSS WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.26         3.48         3.68        18.35         1.38        30.71 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        7.10         7.43         0.07 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             29.00              30.71 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3.24               3.68 
[1] "0.0 - 29.0 (3.2)" "0.1 - 30.7 (3.7)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D40V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED          2         2         2          0          0
  11Q LOSS WILD-TYPE        0         1         5          4          2
                    vv
clus                 STAGE IIIC
  11Q LOSS MUTATED            1
  11Q LOSS WILD-TYPE          0
D40V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  11Q LOSS MUTATED    2  2     3
  11Q LOSS WILD-TYPE  2  5     5
D40V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   2                  2
  T2                   2                  5
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  11Q LOSS MUTATED    4        3
  11Q LOSS WILD-TYPE  3        9
D40V5, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                      4                  3
  N1+N2+N3                3                  9
D40V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    1  6
  11Q LOSS WILD-TYPE  2 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    6
  11Q LOSS WILD-TYPE    2   10
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  6                 10
D40V7, continuous

Clustering(41) Variable = 12P LOSS MUTATION ANALYSIS
D41V1, survival
                    sevent
clus2                0 1
  12P LOSS MUTATED   2 2
  12P LOSS WILD-TYPE 8 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 11 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                  3 
$`12P LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        0.26         1.38        30.71         7.10 

$`12P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         3.48         3.68         4.08        18.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16        29.00         7.43         0.13         0.07 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.26               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             30.71              29.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              4.24               3.48 
[1] "0.3 - 30.7 (4.2)" "0.0 - 29.0 (3.5)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D41V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  12P LOSS MUTATED          0         0         2          1          1
  12P LOSS WILD-TYPE        2         3         5          3          1
                    vv
clus                 STAGE IIIC
  12P LOSS MUTATED            0
  12P LOSS WILD-TYPE          1
D41V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  12P LOSS MUTATED    0  3     1
  12P LOSS WILD-TYPE  4  4     7
D41V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                   0                  4
  T2                   3                  4
  T3+T4                1                  7
                    vv
clus                 N0 N1+N2+N3
  12P LOSS MUTATED    0        4
  12P LOSS WILD-TYPE  7        8
D41V5, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                      0                  7
  N1+N2+N3                4                  8
D41V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  2
  12P LOSS WILD-TYPE  1 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    2
  12P LOSS WILD-TYPE    1   14
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                  1
  MALE                  2                 14
D41V7, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 10 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A4P3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OU         TCGA-L5-A4OX 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-LN-A4A9 
"12P LOSS WILD-TYPE" 

Clustering(42) Variable = 12Q LOSS MUTATION ANALYSIS
D42V1, survival
                    sevent
clus2                0 1
  12Q LOSS MUTATED   2 1
  12Q LOSS WILD-TYPE 8 4
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 12 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                  4 
$`12Q LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OS TCGA-L5-A4OW 
        0.26        30.71         7.10 

$`12Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         3.48         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        1.38         3.16        29.00         7.43         0.13         0.07 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.26               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             30.71              29.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               7.1                3.4 
[1] "0.3 - 30.7 (7.1)" "0.0 - 29.0 (3.4)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D42V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED          0         0         2          0          1
  12Q LOSS WILD-TYPE        2         3         5          4          1
                    vv
clus                 STAGE IIIC
  12Q LOSS MUTATED            0
  12Q LOSS WILD-TYPE          1
D42V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  12Q LOSS MUTATED    0  2     1
  12Q LOSS WILD-TYPE  4  5     7
D42V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                   0                  4
  T2                   2                  5
  T3+T4                1                  7
                    vv
clus                 N0 N1+N2+N3
  12Q LOSS MUTATED    0        3
  12Q LOSS WILD-TYPE  7        9
D42V5, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                      0                  7
  N1+N2+N3                3                  9
D42V6, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  1
  12Q LOSS WILD-TYPE  1 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    1
  12Q LOSS WILD-TYPE    1   15
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                2                  1
  MALE                  1                 15
D42V7, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 11 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A4P3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OM         TCGA-L5-A4ON 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 

Clustering(43) Variable = 13Q LOSS MUTATION ANALYSIS
D43V1, survival
                    sevent
clus2                0 1
  13Q LOSS MUTATED   6 1
  13Q LOSS WILD-TYPE 4 4
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                  8 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  4 
$`13Q LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
        0.26         3.48         3.68         4.08         3.16        29.00 
TCGA-LN-A4A2 
        0.13 

$`13Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        0.03        18.35         3.32         1.38        30.71         7.10 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.13               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             29.00              30.71 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              3.48               5.21 
[1] "0.1 - 29.0 (3.5)" "0.0 - 30.7 (5.2)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D43V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED          2         2         2          2          2
  13Q LOSS WILD-TYPE        0         1         5          2          0
                    vv
clus                 STAGE IIIC
  13Q LOSS MUTATED            0
  13Q LOSS WILD-TYPE          1
D43V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  13Q LOSS MUTATED    3  1     6
  13Q LOSS WILD-TYPE  1  6     2
D43V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   3                  1
  T2                   1                  6
  T3+T4                6                  2
                    vv
clus                 N0 N1+N2+N3
  13Q LOSS MUTATED    6        4
  13Q LOSS WILD-TYPE  1        8
D43V5, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                      6                  1
  N1+N2+N3                4                  8
D43V6, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   1 9
  13Q LOSS WILD-TYPE 2 7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    9
  13Q LOSS WILD-TYPE    2    7
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  9                  7
D43V7, continuous

Clustering(44) Variable = 14Q LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                0 1
  14Q LOSS MUTATED   3 1
  14Q LOSS WILD-TYPE 7 4
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                 11 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  4 
$`14Q LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OU TCGA-L5-A4OW 
        3.48         3.68        29.00         7.10 

$`14Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         0.26         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16        30.71         7.43         0.13         0.07 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              3.48               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             29.00              30.71 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              5.39               3.16 
[1] "3.5 - 29.0 (5.4)" "0.0 - 30.7 (3.2)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D44V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED          0         1         2          0          1
  14Q LOSS WILD-TYPE        2         2         5          4          1
                    vv
clus                 STAGE IIIC
  14Q LOSS MUTATED            0
  14Q LOSS WILD-TYPE          1
D44V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  14Q LOSS MUTATED    1  1     2
  14Q LOSS WILD-TYPE  3  6     6
D44V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                2                  6
                    vv
clus                 N0 N1+N2+N3
  14Q LOSS MUTATED    1        3
  14Q LOSS WILD-TYPE  6        9
D44V5, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                      1                  6
  N1+N2+N3                3                  9
D44V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    1  3
  14Q LOSS WILD-TYPE  2 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1    3
  14Q LOSS WILD-TYPE    2   13
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  3                 13
D44V7, continuous

Clustering(45) Variable = 15Q LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                0 1
  15Q LOSS MUTATED   5 0
  15Q LOSS WILD-TYPE 5 5
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  5 
$`15Q LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OU 
        0.03         0.26         3.48         4.08        29.00 

$`15Q LOSS WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        3.68        18.35         3.32         1.38         3.16        30.71 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         7.43         0.13         0.07 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.03               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             29.00              30.71 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              3.48               3.50 
[1] "0.0 - 29.0 (3.5)" "0.1 - 30.7 (3.5)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr="     "8.3e+08"
D45V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED          1         1         1          0          2
  15Q LOSS WILD-TYPE        1         2         6          4          0
                    vv
clus                 STAGE IIIC
  15Q LOSS MUTATED            0
  15Q LOSS WILD-TYPE          1
D45V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  15Q LOSS MUTATED    1  1     3
  15Q LOSS WILD-TYPE  3  6     5
D45V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  15Q LOSS MUTATED    2        3
  15Q LOSS WILD-TYPE  5        9
D45V5, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                      2                  5
  N1+N2+N3                3                  9
D45V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  4
  15Q LOSS WILD-TYPE  2 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    4
  15Q LOSS WILD-TYPE    2   12
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  4                 12
D45V7, continuous

Clustering(46) Variable = 16P LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                0 1
  16P LOSS MUTATED   2 1
  16P LOSS WILD-TYPE 8 4
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 12 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                  4 
$`16P LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OR TCGA-L5-A4OS 
        3.48         3.16        30.71 

$`16P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        1.38        29.00         7.10         7.43         0.13         0.07 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              3.16               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             30.71              29.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              3.48               3.50 
[1] "3.2 - 30.7 (3.5)" "0.0 - 29.0 (3.5)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D46V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  16P LOSS MUTATED          1         0         1          0          1
  16P LOSS WILD-TYPE        1         3         6          4          1
                    vv
clus                 STAGE IIIC
  16P LOSS MUTATED            0
  16P LOSS WILD-TYPE          1
D46V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  16P LOSS MUTATED    1  1     1
  16P LOSS WILD-TYPE  3  6     7
D46V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                1                  7
                    vv
clus                 N0 N1+N2+N3
  16P LOSS MUTATED    1        2
  16P LOSS WILD-TYPE  6       10
D46V5, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                      1                  6
  N1+N2+N3                2                 10
D46V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  2
  16P LOSS WILD-TYPE  2 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    2
  16P LOSS WILD-TYPE    2   14
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  2                 14
D46V7, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 11 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A4P3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 

Clustering(47) Variable = 16Q LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                0 1
  16Q LOSS MUTATED   2 1
  16Q LOSS WILD-TYPE 8 4
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                 12 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  4 
$`16Q LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OR TCGA-L5-A4OS 
        3.48         3.16        30.71 

$`16Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        1.38        29.00         7.10         7.43         0.13         0.07 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              3.16               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             30.71              29.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              3.48               3.50 
[1] "3.2 - 30.7 (3.5)" "0.0 - 29.0 (3.5)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D47V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED          1         0         1          0          1
  16Q LOSS WILD-TYPE        1         3         6          4          1
                    vv
clus                 STAGE IIIC
  16Q LOSS MUTATED            0
  16Q LOSS WILD-TYPE          1
D47V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  16Q LOSS MUTATED    1  1     1
  16Q LOSS WILD-TYPE  3  6     7
D47V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                1                  7
                    vv
clus                 N0 N1+N2+N3
  16Q LOSS MUTATED    1        2
  16Q LOSS WILD-TYPE  6       10
D47V5, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                      1                  6
  N1+N2+N3                2                 10
D47V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  2
  16Q LOSS WILD-TYPE  2 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    2
  16Q LOSS WILD-TYPE    2   14
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  2                 14
D47V7, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 11 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A4P3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OU         TCGA-L5-A4OW 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 

Clustering(48) Variable = 17P LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                0 1
  17P LOSS MUTATED   5 2
  17P LOSS WILD-TYPE 5 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                  8 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                  3 
$`17P LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OW 
        0.03         0.26         3.48         3.68         3.32         7.10 
TCGA-L5-A4OX 
        7.43 

$`17P LOSS WILD-TYPE`
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        4.08        18.35         1.38         3.16        30.71        29.00 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              7.43              30.71 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              3.48               3.62 
[1] "0.0 - 7.4 (3.5)"  "0.1 - 30.7 (3.6)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D48V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  17P LOSS MUTATED          0         0         4          0          2
  17P LOSS WILD-TYPE        2         3         3          4          0
                    vv
clus                 STAGE IIIC
  17P LOSS MUTATED            1
  17P LOSS WILD-TYPE          0
D48V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  17P LOSS MUTATED    1  3     3
  17P LOSS WILD-TYPE  3  4     5
D48V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   1                  3
  T2                   3                  4
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  17P LOSS MUTATED    0        7
  17P LOSS WILD-TYPE  7        5
D48V5, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                      0                  7
  N1+N2+N3                7                  5
D48V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1  6
  17P LOSS WILD-TYPE  2 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    6
  17P LOSS WILD-TYPE    2   10
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                1                  2
  MALE                  6                 10
D48V7, continuous

Clustering(49) Variable = 18P LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                0 1
  18P LOSS MUTATED   2 0
  18P LOSS WILD-TYPE 8 5
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                  5 
$`18P LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OF 
        3.48         3.68 

$`18P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         0.26         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        3.16        30.71        29.00         7.10         7.43         0.13 
TCGA-LN-A4A9 
        0.07 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3.48               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3.68              30.71 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3.58               3.32 
[1] "3.5 - 3.7 (3.6)"  "0.0 - 30.7 (3.3)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 13 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OR         TCGA-L5-A4OS         TCGA-L5-A4OU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-LN-A4A2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-LN-A4A9 
"18P LOSS WILD-TYPE" 
D49V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  18P LOSS MUTATED          0         0         1          2          1
  18P LOSS WILD-TYPE        2         3         6          2          1
                    vv
clus                 STAGE IIIC
  18P LOSS MUTATED            0
  18P LOSS WILD-TYPE          1
D49V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  18P LOSS MUTATED    1  0     3
  18P LOSS WILD-TYPE  3  7     5
D49V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                   1                  3
  T2                   0                  7
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  18P LOSS MUTATED    1        3
  18P LOSS WILD-TYPE  6        9
D49V5, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                      1                  6
  N1+N2+N3                3                  9
D49V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    0  4
  18P LOSS WILD-TYPE  3 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    4
  18P LOSS WILD-TYPE    3   12
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                0                  3
  MALE                  4                 12
D49V7, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 10 
        TCGA-IG-A3YA         TCGA-IG-A4P3         TCGA-L5-A4OM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-LN-A4A9 
"18P LOSS WILD-TYPE" 

Clustering(50) Variable = 18Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                0 1
  18Q LOSS MUTATED   5 1
  18Q LOSS WILD-TYPE 5 4
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                  9 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  4 
$`18Q LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A4OX 
        0.26         3.48         3.68         3.32        29.00         7.43 

$`18Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         4.08        18.35         1.38         3.16        30.71 
TCGA-L5-A4OW TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         0.13         0.07 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.26               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             29.00              30.71 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3.58               3.16 
[1] "0.3 - 29.0 (3.6)" "0.0 - 30.7 (3.2)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "3.2"
D50V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED          0         1         2          2          2
  18Q LOSS WILD-TYPE        2         2         5          2          0
                    vv
clus                 STAGE IIIC
  18Q LOSS MUTATED            1
  18Q LOSS WILD-TYPE          0
D50V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  18Q LOSS MUTATED    1  1     6
  18Q LOSS WILD-TYPE  3  6     2
D50V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                   1                  3
  T2                   1                  6
  T3+T4                6                  2
                    vv
clus                 N0 N1+N2+N3
  18Q LOSS MUTATED    2        6
  18Q LOSS WILD-TYPE  5        6
D50V5, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                      2                  5
  N1+N2+N3                6                  6
D50V6, binary
                    cls
clus                 0 1
  18Q LOSS MUTATED   0 8
  18Q LOSS WILD-TYPE 3 8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0    8
  18Q LOSS WILD-TYPE    3    8
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                0                  3
  MALE                  8                  8
D50V7, continuous

Clustering(51) Variable = 19P LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                0 1
  19P LOSS MUTATED   5 1
  19P LOSS WILD-TYPE 5 4
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                  9 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                  4 
$`19P LOSS MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 
        0.26         3.68         4.08        30.71         7.43         0.13 

$`19P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.03         3.48        18.35         3.32         1.38         3.16 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
       29.00         7.10         0.07 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.13               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             30.71              29.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3.88               3.32 
[1] "0.1 - 30.7 (3.9)" "0.0 - 29.0 (3.3)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D51V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  19P LOSS MUTATED          1         1         4          1          1
  19P LOSS WILD-TYPE        1         2         3          3          1
                    vv
clus                 STAGE IIIC
  19P LOSS MUTATED            0
  19P LOSS WILD-TYPE          1
D51V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  19P LOSS MUTATED    2  3     3
  19P LOSS WILD-TYPE  2  4     5
D51V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                   2                  2
  T2                   3                  4
  T3+T4                3                  5
                    vv
clus                 N0 N1+N2+N3
  19P LOSS MUTATED    2        6
  19P LOSS WILD-TYPE  5        6
D51V5, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                      2                  5
  N1+N2+N3                6                  6
D51V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  6
  19P LOSS WILD-TYPE  1 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    6
  19P LOSS WILD-TYPE    1   10
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                2                  1
  MALE                  6                 10
D51V7, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 10 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A4P3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4ON         TCGA-L5-A4OO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-LN-A4A9 
"19P LOSS WILD-TYPE" 

Clustering(52) Variable = 19Q LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                0 1
  19Q LOSS MUTATED   3 1
  19Q LOSS WILD-TYPE 7 4
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 11 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                  4 
$`19Q LOSS MUTATED`
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 
        4.08        30.71         7.43         0.13 

$`19Q LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.48         3.68        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
        1.38         3.16        29.00         7.10         0.07 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.13               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             30.71              29.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             5.755              3.320 
[1] "0.1 - 30.7 (5.8)" "0.0 - 29.0 (3.3)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D52V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED          1         1         2          1          0
  19Q LOSS WILD-TYPE        1         2         5          3          2
                    vv
clus                 STAGE IIIC
  19Q LOSS MUTATED            0
  19Q LOSS WILD-TYPE          1
D52V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  19Q LOSS MUTATED    1  2     2
  19Q LOSS WILD-TYPE  3  5     6
D52V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   1                  3
  T2                   2                  5
  T3+T4                2                  6
                    vv
clus                 N0 N1+N2+N3
  19Q LOSS MUTATED    2        3
  19Q LOSS WILD-TYPE  5        9
D52V5, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                      2                  5
  N1+N2+N3                3                  9
D52V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  3
  19Q LOSS WILD-TYPE  1 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    3
  19Q LOSS WILD-TYPE    1   13
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                2                  1
  MALE                  3                 13
D52V7, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 10 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A4P3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4ON         TCGA-L5-A4OO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OU         TCGA-L5-A4OW 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-LN-A4A9 
"19Q LOSS WILD-TYPE" 

Clustering(53) Variable = 21Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                0 1
  21Q LOSS MUTATED   6 3
  21Q LOSS WILD-TYPE 4 2
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                  6 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                  2 
$`21Q LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         0.26         3.48         4.08         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       29.00         7.10         7.43 

$`21Q LOSS WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.68        18.35         3.32         1.38         0.13         0.07 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.03               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             30.71              18.35 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              4.08               2.35 
[1] "0.0 - 30.7 (4.1)" "0.1 - 18.4 (2.3)"
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D53V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED          2         1         4          2          2
  21Q LOSS WILD-TYPE        0         2         3          2          0
                    vv
clus                 STAGE IIIC
  21Q LOSS MUTATED            0
  21Q LOSS WILD-TYPE          1
D53V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  21Q LOSS MUTATED    2  4     5
  21Q LOSS WILD-TYPE  2  3     3
D53V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                   2                  2
  T2                   4                  3
  T3+T4                5                  3
                    vv
clus                 N0 N1+N2+N3
  21Q LOSS MUTATED    5        6
  21Q LOSS WILD-TYPE  2        6
D53V5, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                      5                  2
  N1+N2+N3                6                  6
D53V6, binary
                    cls
clus                 0 1
  21Q LOSS MUTATED   3 8
  21Q LOSS WILD-TYPE 0 8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    8
  21Q LOSS WILD-TYPE    0    8
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                3                  0
  MALE                  8                  8
D53V7, continuous

Clustering(54) Variable = 22Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                0 1
  22Q LOSS MUTATED   5 2
  22Q LOSS WILD-TYPE 5 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                  8 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                  3 
$`22Q LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OS TCGA-L5-A4OU 
        0.03         0.26         3.48        18.35        30.71        29.00 
TCGA-L5-A4OW 
        7.10 

$`22Q LOSS WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OX 
        3.68         4.08         3.32         1.38         3.16         7.43 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.03               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             30.71               7.43 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              7.10               3.24 
[1] "0.0 - 30.7 (7.1)" "0.1 - 7.4 (3.2)" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-L5-A4OE 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OF         TCGA-L5-A4OM         TCGA-L5-A4ON 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OO         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OU         TCGA-L5-A4OW 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-L5-A4OX         TCGA-LN-A4A2         TCGA-LN-A4A9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "6"  
D54V2, continuous
                    vv
clus                 STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED          0         1         4          1          2
  22Q LOSS WILD-TYPE        2         2         3          3          0
                    vv
clus                 STAGE IIIC
  22Q LOSS MUTATED            0
  22Q LOSS WILD-TYPE          1
D54V3, multiclass
                    vv
clus                 T1 T2 T3+T4
  22Q LOSS MUTATED    1  3     4
  22Q LOSS WILD-TYPE  3  4     4
D54V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                   1                  3
  T2                   3                  4
  T3+T4                4                  4
                    vv
clus                 N0 N1+N2+N3
  22Q LOSS MUTATED    1        7
  22Q LOSS WILD-TYPE  6        5
D54V5, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                      1                  6
  N1+N2+N3                7                  5
D54V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    2  6
  22Q LOSS WILD-TYPE  1 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2    6
  22Q LOSS WILD-TYPE    1   10
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                2                  1
  MALE                  6                 10
D54V7, continuous
> q(save="no")
