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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/18/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/18/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/CESC-TP/2735926/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2587644/1.GDAC_clinicalDataPicker.Finished/CESC-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=CESC-TP", "-nV=Nozzle.R1", "-OP=", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=CESC-TP"
[1] "opt"  "-OP="
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt" ""   
[1] "dx" ""  

nPatients in clinical file=40, in cluster file=114, common to both=34
[1] "Reduce the number of clustering variables from 80 to 44."
[1] 44 34
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                27 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                27 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15                19 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15                19 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                31 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                31 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                31 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                31 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               21                13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               21                13 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9                25 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9                25 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                28 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                28 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                30 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                30 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                30 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                27 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                27 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 31 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 31 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 28 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 30 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 31 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 31 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 31 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 31 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 30 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 31 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 31 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 31 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 28 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 28 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 23 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 23 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                 22 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                 22 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 31 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 31 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 29 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 29 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                25 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                25 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14                20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14                20 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                29 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                29 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                24 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                24 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                30 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                30 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                30 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                30 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                24 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                24 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                30 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                31 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                31 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                 27 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                 27 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                 28 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                 28 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 27 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 27 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 27 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 28 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 28 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                 26 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                 26 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 24 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 24 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 31 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 31 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 28 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 28 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 27 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 27 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 30 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 30 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 28 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 28 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "DISTANT.METASTASIS"                    
[15] "LYMPH.NODE.METASTASIS"                 
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "TUMOR.STAGECODE"                       
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 34 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
        1505          925         5385           NA           NA         1616 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
          NA           NA           NA         2382         2155         1289 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT 
          NA           81         2127         2892          183            8 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 
          53           40           25           19           NA          178 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
         211           37           37           30           66            2 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
          31           44          773          168 
Variable 1:'AGE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'STOPPEDSMOKINGYEAR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "HISTOLOGICAL.TYPE"                     
 [3] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [4] "NUMBERPACKYEARSSMOKED"                 
 [5] "STOPPEDSMOKINGYEAR"                    
 [6] "TOBACCOSMOKINGHISTORYINDICATOR"        
 [7] "DISTANT.METASTASIS"                    
 [8] "LYMPH.NODE.METASTASIS"                 
 [9] "NUMBER.OF.LYMPH.NODES"                 
[10] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "10"          
[1] "stage2"
vv
 T1B T1B1 T1B2  T2A T2A1 T2A2  T2B  T3B 
   5   10    4    2    2    1    5    1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 34 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=27, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=9, binary=FALSE, numeric=TRUE
STOPPEDSMOKINGYEAR, nv=4, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=4, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    6  1
  1P GAIN WILD-TYPE 21  5
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                26 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 5 
$`1P GAIN MUTATED`
TCGA-C5-A1BK TCGA-C5-A1MK TCGA-DR-A0ZL TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-FU-A3NI 
      177.04         2.43        70.85         1.74         0.62         1.45 
TCGA-HM-A3JK 
        5.52 

$`1P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41         5.46        67.46        53.13        35.61 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.93        78.31        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EX-A1H5 
       95.08         6.02         0.26         1.32         0.82         5.85 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA 
        1.02        25.41 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.62              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           177.04             95.08 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.43              6.48 
[1] "0.6 - 177.0 (2.4)" "0.1 - 95.1 (6.5)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "1P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "1P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "1P GAIN MUTATED" 
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                  4
  1P GAIN WILD-TYPE                               23
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                     0                       3
  1P GAIN WILD-TYPE                                   1                       3
D1V3, multiclass
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    5
  1P GAIN WILD-TYPE    8   19
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                2                 8
  YES               5                19
D1V5, continuous
D1V6, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-DS-A3LQ        TCGA-FU-A2QG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V7, continuous
D1V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    3
  1P GAIN WILD-TYPE   17    6
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               3                17
  MX               3                 6
D1V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    2
  1P GAIN WILD-TYPE   15    9
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               4                15
  N1               2                 9
D1V10, continuous
D1V11, continuous

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   12  2
  1Q GAIN WILD-TYPE 15  4
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               14                19 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                 4 
$`1Q GAIN MUTATED`
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL 
      177.04         5.46        53.13         2.43        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-FU-A23L TCGA-FU-A3EO 
       42.38         6.02         1.74         0.62         1.22         2.17 
TCGA-FU-A3NI TCGA-HM-A3JK 
        1.45         5.52 

$`1Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DS-A0VK 
       49.48        30.41        67.46        35.61        40.93        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
        2.66        69.93        95.08         0.26         1.32         0.82 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        5.85         6.94         1.22         0.99         0.07         1.02 
TCGA-HG-A2PA 
       25.41 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.62              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           177.04             95.08 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             5.49              6.94 
[1] "0.6 - 177.0 (5.5)" "0.1 - 95.1 (6.9)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "1Q GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "1Q GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "1Q GAIN MUTATED" 
[1] "hr=" "1.7"
D2V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                 10
  1Q GAIN WILD-TYPE                               17
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                     1                       4
  1Q GAIN WILD-TYPE                                   0                       2
D2V3, multiclass
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    9
  1Q GAIN WILD-TYPE    4   15
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                6                 4
  YES               9                15
D2V5, continuous
D2V6, continuous
[1] "Remove cluster labels:" "1Q GAIN WILD-TYPE"     
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                 2 
     TCGA-C5-A1MF      TCGA-DS-A3LQ      TCGA-HM-A3JK 
"1Q GAIN MUTATED" "1Q GAIN MUTATED" "1Q GAIN MUTATED" 
D2V7, continuous
D2V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    6
  1Q GAIN WILD-TYPE   14    3
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               6                14
  MX               6                 3
D2V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    4
  1Q GAIN WILD-TYPE   11    7
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               8                11
  N1               4                 7
D2V10, continuous
D2V11, continuous

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    2  1
  2P GAIN WILD-TYPE 25  5
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 5 
$`2P GAIN MUTATED`
TCGA-C5-A1BN TCGA-DS-A3LQ TCGA-FU-A23L 
        5.46         6.02         1.22 

$`2P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41       177.04        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        69.93        95.08         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG 
        0.82         0.62         5.85         6.94         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02         1.45        25.41         5.52 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.22              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             6.02            177.04 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            5.460             6.395 
[1] "1.2 - 6.0 (5.5)"   "0.1 - 177.0 (6.4)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" 
[1] "hr=" "9"  
D3V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                  2
  2P GAIN WILD-TYPE                               25
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                     0                       1
  2P GAIN WILD-TYPE                                   1                       5
D3V3, multiclass
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    1
  2P GAIN WILD-TYPE    8   23
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                2                 8
  YES               1                23
D3V5, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 9 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HY 
"2P GAIN WILD-TYPE" 
D3V6, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-FU-A2QG        TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
D3V7, continuous
D3V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    1
  2P GAIN WILD-TYPE   19    8
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               1                19
  MX               1                 8
D3V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    1
  2P GAIN WILD-TYPE   18   10
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               1                18
  N1               1                10
D3V10, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                28 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1M5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA        TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
D3V11, continuous

Clustering(4) Variable = 3p gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3  0
  3P GAIN WILD-TYPE 24  6
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                30 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 6 
$`3P GAIN MUTATED`
TCGA-DS-A0VL TCGA-FU-A3NI TCGA-HM-A3JK 
        2.66         1.45         5.52 

$`3P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76        69.93        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K 
        1.32         0.82         0.62         5.85         6.94         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        1.22         0.99         2.17         0.07         1.02        25.41 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.45              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             5.52            177.04 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.66              6.48 
[1] "1.4 - 5.5 (2.7)"   "0.1 - 177.0 (6.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "3P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "3P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "3P GAIN MUTATED" 
[1] "hr="     "2.8e+07"
D4V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                  1
  3P GAIN WILD-TYPE                               26
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                     0                       2
  3P GAIN WILD-TYPE                                   1                       4
D4V3, multiclass
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE    9   22
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                1                 9
  YES               2                22
D4V5, continuous
D4V6, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-DS-A3LQ        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D4V7, continuous
D4V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE   19    7
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               1                19
  MX               2                 7
D4V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE   18    9
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               1                18
  N1               2                 9
D4V10, continuous
D4V11, continuous

Clustering(5) Variable = 3q gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   17  3
  3Q GAIN WILD-TYPE 10  3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               20                13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                 3 
$`3Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LY 
       49.48       177.04        67.46        53.13         2.43        78.31 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT 
       70.85        36.76         2.66        69.93        95.08         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-FU-A23L 
        1.74         1.32         0.82         0.62         5.85         1.22 
TCGA-FU-A3NI TCGA-HM-A3JK 
        1.45         5.52 

$`3Q GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DR-A0ZM TCGA-DS-A3LQ 
       30.41         5.46        35.61        40.93        42.38         6.02 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.94         1.22         0.99         2.17         0.07         1.02 
TCGA-HG-A2PA 
       25.41 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.26              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           177.04             42.38 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            5.685             6.020 
[1] "0.3 - 177.0 (5.7)" "0.1 - 42.4 (6.0)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "3Q GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "3Q GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
  "3Q GAIN MUTATED" 
[1] "hr=" "4"  
D5V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                 18
  3Q GAIN WILD-TYPE                                9
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                     0                       3
  3Q GAIN WILD-TYPE                                   1                       3
D5V3, multiclass
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6   15
  3Q GAIN WILD-TYPE    4    9
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                6                 4
  YES              15                 9
D5V5, continuous
D5V6, continuous
[1] "Remove cluster labels:" "3Q GAIN WILD-TYPE"     
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                 2 
     TCGA-BI-A0VR      TCGA-C5-A1MF      TCGA-HM-A3JK 
"3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" 
D5V7, continuous
D5V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13    6
  3Q GAIN WILD-TYPE    7    3
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              13                 7
  MX               6                 3
D5V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13    6
  3Q GAIN WILD-TYPE    6    5
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              13                 6
  N1               6                 5
D5V10, continuous
D5V11, continuous

Clustering(6) Variable = 5p gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    7  1
  5P GAIN WILD-TYPE 20  5
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                25 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 5 
$`5P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1MN TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EX-A1H5 TCGA-FU-A23L 
       30.41        40.93         6.02         1.32         5.85         1.22 
TCGA-FU-A3HY TCGA-FU-A3NI 
        0.07         1.45 

$`5P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48       177.04         5.46        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       69.93        95.08         0.26         1.74         0.82         0.62 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-HG-A2PA 
        6.94         1.22         0.99         2.17         1.02        25.41 
TCGA-HM-A3JK 
        5.52 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.26 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            40.93            177.04 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             3.65              6.94 
[1] "0.1 - 40.9 (3.6)"  "0.3 - 177.0 (6.9)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D6V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                  6
  5P GAIN WILD-TYPE                               21
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                     0                       3
  5P GAIN WILD-TYPE                                   1                       3
D6V3, multiclass
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    6
  5P GAIN WILD-TYPE    7   18
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                3                 7
  YES               6                18
D6V5, continuous
D6V6, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-FU-A2QG        TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D6V7, continuous
D6V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    4
  5P GAIN WILD-TYPE   17    5
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               3                17
  MX               4                 5
D6V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    4
  5P GAIN WILD-TYPE   16    7
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               3                16
  N1               4                 7
D6V10, continuous
D6V11, continuous

Clustering(7) Variable = 6p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    4  2
  6P GAIN WILD-TYPE 23  4
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                27 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                 4 
$`6P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A2LY TCGA-FU-A23K TCGA-FU-A23L 
       30.41         5.46        35.61        78.31         1.22         1.22 

$`6P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN 
       49.48       177.04        67.46        53.13         2.43        40.93 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       70.85        42.38        36.76         2.66        69.93        95.08 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        6.02         0.26         1.74         1.32         0.82         0.62 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        5.85         6.94         0.99         2.17         0.07         1.02 
TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        1.45        25.41         5.52 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.22              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            78.31            177.04 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           17.935             5.850 
[1] "1.2 - 78.3 (17.9)" "0.1 - 177.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D7V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                  6
  6P GAIN WILD-TYPE                               21
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                     0                       0
  6P GAIN WILD-TYPE                                   1                       6
D7V3, multiclass
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    3
  6P GAIN WILD-TYPE    7   21
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                3                 7
  YES               3                21
D7V5, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                 8 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-C5-A1MN        TCGA-DR-A0ZM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D7V6, continuous
D7V7, continuous
D7V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    2
  6P GAIN WILD-TYPE   17    7
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               3                17
  MX               2                 7
D7V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    2
  6P GAIN WILD-TYPE   16    9
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               3                16
  N1               2                 9
D7V10, continuous
D7V11, continuous

Clustering(8) Variable = 7q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    4  0
  7Q GAIN WILD-TYPE 23  6
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                29 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 6 
$`7Q GAIN MUTATED`
TCGA-C5-A1MF TCGA-C5-A2LY TCGA-DS-A3LQ TCGA-FU-A3NI 
       53.13        78.31         6.02         1.45 

$`7Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MI 
       49.48        30.41       177.04         5.46        67.46        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        40.93        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       69.93        95.08         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.62         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02        25.41         5.52 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.45              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            78.31            177.04 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           29.575             5.520 
[1] "1.4 - 78.3 (29.6)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" 
[1] "hr="     "2.4e+08"
D8V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                  2
  7Q GAIN WILD-TYPE                               25
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                     0                       2
  7Q GAIN WILD-TYPE                                   1                       4
D8V3, multiclass
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    1
  7Q GAIN WILD-TYPE    7   23
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                3                 7
  YES               1                23
D8V5, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                 9 
       TCGA-BI-A0VR        TCGA-C5-A1BN        TCGA-C5-A1MI        TCGA-C5-A1MN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY 
"7Q GAIN WILD-TYPE" 
D8V6, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                 3 
       TCGA-BI-A0VR        TCGA-FU-A2QG        TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
D8V7, continuous
D8V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    2
  7Q GAIN WILD-TYPE   18    7
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               2                18
  MX               2                 7
D8V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    2
  7Q GAIN WILD-TYPE   17    9
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0               2                17
  N1               2                 9
D8V10, continuous
D8V11, continuous

Clustering(9) Variable = 8p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    3  1
  8P GAIN WILD-TYPE 24  5
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                29 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 5 
$`8P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-DS-A3LQ TCGA-EA-A3HQ 
       30.41        67.46         6.02         1.74 

$`8P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK 
       49.48       177.04         5.46        53.13        35.61         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       40.93        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       69.93        95.08         0.26         1.32         0.82         0.62 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.74              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            67.46            177.04 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           18.215             5.520 
[1] "1.7 - 67.5 (18.2)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D9V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                  3
  8P GAIN WILD-TYPE                               24
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                     0                       1
  8P GAIN WILD-TYPE                                   1                       5
D9V3, multiclass
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    3
  8P GAIN WILD-TYPE    9   21
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                1                 9
  YES               3                21
D9V5, continuous
D9V6, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-FU-A2QG        TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D9V7, continuous
D9V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    0
  8P GAIN WILD-TYPE   16    9
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               4                16
  MX               0                 9
D9V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    1
  8P GAIN WILD-TYPE   16   10
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               3                16
  N1               1                10
D9V10, continuous
D9V11, continuous

Clustering(10) Variable = 8q gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    6  1
  8Q GAIN WILD-TYPE 21  5
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 5 
$`8Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ 
       30.41        67.46        53.13        69.93         6.02         1.74 
TCGA-FU-A3NI 
        1.45 

$`8Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN 
       49.48       177.04         5.46        35.61         2.43        40.93 
TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN 
       78.31        70.85        42.38        36.76         2.66        95.08 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 
        0.26         1.32         0.82         0.62         5.85         6.94 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22         1.22         0.99         2.17         0.07         1.02 
TCGA-HG-A2PA TCGA-HM-A3JK 
       25.41         5.52 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1.45              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            69.93            177.04 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            30.41              5.49 
[1] "1.4 - 69.9 (30.4)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D10V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                  5
  8Q GAIN WILD-TYPE                               22
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                     0                       2
  8Q GAIN WILD-TYPE                                   1                       4
D10V3, multiclass
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    5
  8Q GAIN WILD-TYPE    8   19
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                2                 8
  YES               5                19
D10V5, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 9 
       TCGA-BI-A0VR        TCGA-C5-A1BN        TCGA-C5-A1MI        TCGA-C5-A1MN 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY 
"8Q GAIN WILD-TYPE" 
D10V6, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 3 
       TCGA-BI-A0VR        TCGA-FU-A2QG        TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
D10V7, continuous
D10V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    2
  8Q GAIN WILD-TYPE   15    7
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               5                15
  MX               2                 7
D10V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4    3
  8Q GAIN WILD-TYPE   15    8
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0               4                15
  N1               3                 8
D10V10, continuous
D10V11, continuous

Clustering(11) Variable = 10p gain mutation analysis
D11V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    2  1
  10P GAIN WILD-TYPE 25  5
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 30 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                  5 
$`10P GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A0VK TCGA-FU-A3NI 
       30.41        36.76         1.45 

$`10P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48       177.04         5.46        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
        2.43        40.93        78.31        70.85        42.38         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.82         0.62         5.85         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        0.99         2.17         0.07         1.02        25.41         5.52 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.45               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             36.76             177.04 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            30.410              5.685 
[1] "1.4 - 36.8 (30.4)" "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "3.2"
D11V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                  2
  10P GAIN WILD-TYPE                               25
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P GAIN MUTATED                                     0
  10P GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                         1
  10P GAIN WILD-TYPE                       5
D11V3, multiclass
D11V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    3
  10P GAIN WILD-TYPE   10   21
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 0                 10
  YES                3                 21
D11V5, continuous
D11V6, continuous
D11V7, continuous
D11V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    1
  10P GAIN WILD-TYPE   18    8
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                2                 18
  MX                1                  8
D11V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE   18    9
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                1                 18
  N1                2                  9
D11V10, continuous
D11V11, continuous

Clustering(12) Variable = 12p gain mutation analysis
D12V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    6  0
  12P GAIN WILD-TYPE 21  6
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 27 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  6 
$`12P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1MF TCGA-DS-A3LQ TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI 
       30.41        53.13         6.02         1.22         2.17         1.45 

$`12P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MI TCGA-C5-A1MK 
       49.48       177.04         5.46        67.46        35.61         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       40.93        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       69.93        95.08         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY 
        0.62         5.85         6.94         1.22         0.99         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02        25.41         5.52 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.22               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             53.13             177.04 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             4.095              5.850 
[1] "1.2 - 53.1 (4.1)"  "0.1 - 177.0 (5.8)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr="     "8.1e+07"
D12V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                  3
  12P GAIN WILD-TYPE                               24
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P GAIN MUTATED                                     1
  12P GAIN WILD-TYPE                                   0
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                         2
  12P GAIN WILD-TYPE                       4
D12V3, multiclass
D12V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    4
  12P GAIN WILD-TYPE    8   20
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 2                  8
  YES                4                 20
D12V5, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  8 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D12V6, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D12V7, continuous
D12V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    4
  12P GAIN WILD-TYPE   18    5
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                2                 18
  MX                4                  5
D12V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4    2
  12P GAIN WILD-TYPE   15    9
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                4                 15
  N1                2                  9
D12V10, continuous
D12V11, continuous

Clustering(13) Variable = 12q gain mutation analysis
D13V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    4  0
  12Q GAIN WILD-TYPE 23  6
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 29 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  6 
$`12Q GAIN MUTATED`
TCGA-C5-A1MF TCGA-DS-A3LQ TCGA-FU-A23L TCGA-FU-A3NI 
       53.13         6.02         1.22         1.45 

$`12Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MI 
       49.48        30.41       177.04         5.46        67.46        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        69.93        95.08         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG 
        0.82         0.62         5.85         6.94         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02        25.41         5.52 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.22               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             53.13             177.04 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             3.735              5.850 
[1] "1.2 - 53.1 (3.7)"  "0.1 - 177.0 (5.8)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr="     "7.7e+07"
D13V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                  2
  12Q GAIN WILD-TYPE                               25
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12Q GAIN MUTATED                                     0
  12Q GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                         2
  12Q GAIN WILD-TYPE                       4
D13V3, multiclass
D13V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    2
  12Q GAIN WILD-TYPE    8   22
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 2                  8
  YES                2                 22
D13V5, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  9 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D13V6, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D13V7, continuous
D13V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    3
  12Q GAIN WILD-TYPE   19    6
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                1                 19
  MX                3                  6
D13V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    2
  12Q GAIN WILD-TYPE   17    9
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                2                 17
  N1                2                  9
D13V10, continuous
D13V11, continuous

Clustering(14) Variable = 14q gain mutation analysis
D14V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    2  1
  14Q GAIN WILD-TYPE 25  5
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 30 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  5 
$`14Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1MI TCGA-FU-A3HY 
       30.41        35.61         0.07 

$`14Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48       177.04         5.46        67.46        53.13         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       40.93        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.82         0.62         5.85         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.99         2.17         1.02         1.45        25.41         5.52 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.07               0.26 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             35.61             177.04 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            30.410              5.685 
[1] "0.1 - 35.6 (30.4)" "0.3 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "4.8"
D14V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                  2
  14Q GAIN WILD-TYPE                               25
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  14Q GAIN MUTATED                                     0
  14Q GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                         1
  14Q GAIN WILD-TYPE                       5
D14V3, multiclass
D14V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    2
  14Q GAIN WILD-TYPE    9   22
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 1                  9
  YES                2                 22
D14V5, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  8 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D14V6, continuous
D14V7, continuous
D14V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   18    8
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                2                 18
  MX                1                  8
D14V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    2
  14Q GAIN WILD-TYPE   18    9
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                1                 18
  N1                2                  9
D14V10, continuous
D14V11, continuous

Clustering(15) Variable = 15q gain mutation analysis
D15V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    3  0
  15Q GAIN WILD-TYPE 24  6
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 30 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  6 
$`15Q GAIN MUTATED`
TCGA-EA-A3HQ TCGA-EX-A3L1 TCGA-FU-A23L 
        1.74         6.94         1.22 

$`15Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT 
       36.76         2.66        69.93        95.08         6.02         0.26 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
        1.32         0.82         0.62         5.85         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02         1.45        25.41         5.52 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.22               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              6.94             177.04 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             1.740              5.935 
[1] "1.2 - 6.9 (1.7)"   "0.1 - 177.0 (5.9)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D15V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                  2
  15Q GAIN WILD-TYPE                               25
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  15Q GAIN MUTATED                                     0
  15Q GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                         1
  15Q GAIN WILD-TYPE                       5
D15V3, multiclass
D15V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    3
  15Q GAIN WILD-TYPE   10   21
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                 10
  YES                3                 21
D15V5, continuous
D15V6, continuous
D15V7, continuous
D15V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    1
  15Q GAIN WILD-TYPE   18    8
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                2                 18
  MX                1                  8
D15V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    0
  15Q GAIN WILD-TYPE   16   11
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                3                 16
  N1                0                 11
D15V10, continuous
D15V11, continuous

Clustering(16) Variable = 16p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    3  0
  16P GAIN WILD-TYPE 24  6
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  6 
$`16P GAIN MUTATED`
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-FU-A3NI 
        6.02         1.74         1.45 

$`16P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR 
       36.76         2.66        69.93        95.08         0.26         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.82         0.62         5.85         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        0.99         2.17         0.07         1.02        25.41         5.52 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1.45               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              6.02             177.04 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             1.740              6.395 
[1] "1.4 - 6.0 (1.7)"   "0.1 - 177.0 (6.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D16V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                  2
  16P GAIN WILD-TYPE                               25
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16P GAIN MUTATED                                     0
  16P GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                         2
  16P GAIN WILD-TYPE                       4
D16V3, multiclass
D16V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    3
  16P GAIN WILD-TYPE    9   21
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 1                  9
  YES                3                 21
D16V5, continuous
D16V6, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-FU-A2QG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" 
D16V7, continuous
D16V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    1
  16P GAIN WILD-TYPE   18    8
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                2                 18
  MX                1                  8
D16V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    2
  16P GAIN WILD-TYPE   18    9
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                1                 18
  N1                2                  9
D16V10, continuous
D16V11, continuous

Clustering(17) Variable = 16q gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    2  0
  16Q GAIN WILD-TYPE 25  6
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 0                  6 
$`16Q GAIN MUTATED`
TCGA-DS-A3LQ TCGA-EX-A3L1 
        6.02         6.94 

$`16Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76         2.66        69.93        95.08         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
        1.32         0.82         0.62         5.85         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        0.99         2.17         0.07         1.02         1.45        25.41 
TCGA-HM-A3JK 
        5.52 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              6.02               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              6.94             177.04 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              6.48               5.52 
[1] "6.0 - 6.9 (6.5)"   "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 31 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A23K         TCGA-FU-A23L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-HG-A2PA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" 
D17V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                  1
  16Q GAIN WILD-TYPE                               26
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16Q GAIN MUTATED                                     0
  16Q GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                         2
  16Q GAIN WILD-TYPE                       4
D17V3, multiclass
D17V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    2
  16Q GAIN WILD-TYPE    9   22
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 1                  9
  YES                2                 22
D17V5, continuous
D17V6, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-FU-A2QG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" 
D17V7, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 31 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A23K         TCGA-FU-A23L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-HG-A2PA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" 
D17V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    0
  16Q GAIN WILD-TYPE   18    9
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                2                 18
  MX                0                  9
D17V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    1
  16Q GAIN WILD-TYPE   18   10
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                1                 18
  N1                1                 10
D17V10, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 28 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1MF         TCGA-C5-A1MI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A23K         TCGA-FU-A23L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-HG-A2PA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" 
D17V11, continuous

Clustering(18) Variable = 18p gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    3  0
  18P GAIN WILD-TYPE 24  6
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 30 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  6 
$`18P GAIN MUTATED`
TCGA-DR-A0ZL TCGA-DS-A3LQ TCGA-HM-A3JK 
       70.85         6.02         5.52 

$`18P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK 
       35.61         2.43        40.93        78.31        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        69.93        95.08         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.82         0.62         5.85         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        0.99         2.17         0.07         1.02         1.45        25.41 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              5.52               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             70.85             177.04 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             6.020              5.655 
[1] "5.5 - 70.8 (6.0)"  "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
[1] "hr="     "2.2e+08"
D18V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                  1
  18P GAIN WILD-TYPE                               26
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P GAIN MUTATED                                     0
  18P GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                         2
  18P GAIN WILD-TYPE                       4
D18V3, multiclass
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    1
  18P GAIN WILD-TYPE    8   23
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 2                  8
  YES                1                 23
D18V5, continuous
D18V6, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  3 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-FU-A2QG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D18V7, continuous
D18V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    1
  18P GAIN WILD-TYPE   18    8
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                2                 18
  MX                1                  8
D18V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE   18    9
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                1                 18
  N1                2                  9
D18V10, continuous
D18V11, continuous

Clustering(19) Variable = 19q gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    3  3
  19Q GAIN WILD-TYPE 24  3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 27 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                  3 
$`19Q GAIN MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DS-A3LQ 
        5.46        53.13        35.61         2.43        78.31         6.02 

$`19Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MN TCGA-DR-A0ZL 
       49.48        30.41       177.04        67.46        40.93        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT 
       42.38        36.76         2.66        69.93        95.08         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 
        1.74         1.32         0.82         0.62         5.85         6.94 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22         1.22         0.99         2.17         0.07         1.02 
TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        1.45        25.41         5.52 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              2.43               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             78.31             177.04 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            20.815              5.520 
[1] "2.4 - 78.3 (20.8)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "3.5"
D19V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                  5
  19Q GAIN WILD-TYPE                               22
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19Q GAIN MUTATED                                     0
  19Q GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                         1
  19Q GAIN WILD-TYPE                       5
D19V3, multiclass
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6    0
  19Q GAIN WILD-TYPE    4   24
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 6                  4
  YES                0                 24
D19V5, continuous
D19V6, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D19V7, continuous
D19V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    1
  19Q GAIN WILD-TYPE   17    8
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                3                 17
  MX                1                  8
D19V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    2
  19Q GAIN WILD-TYPE   17    9
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                2                 17
  N1                2                  9
D19V10, continuous
D19V11, continuous

Clustering(20) Variable = 20p gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    8  3
  20P GAIN WILD-TYPE 19  3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 22 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  3 
$`20P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DS-A3LQ TCGA-EA-A3HQ 
       30.41        67.46        35.61        40.93         6.02         1.74 
TCGA-EA-A3HS TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3NI TCGA-HM-A3JK 
        0.82         1.22         2.17         1.45         5.52 

$`20P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LY 
       49.48       177.04         5.46        53.13         2.43        78.31 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       70.85        42.38        36.76         2.66        69.93        95.08 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L 
        0.26         1.32         0.62         5.85         6.94         1.22 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        0.99         0.07         1.02        25.41 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.82               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             67.46             177.04 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             5.520              6.395 
[1] "0.8 - 67.5 (5.5)"  "0.1 - 177.0 (6.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
[1] "hr=" "3.4"
D20V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                  7
  20P GAIN WILD-TYPE                               20
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20P GAIN MUTATED                                     1
  20P GAIN WILD-TYPE                                   0
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                         3
  20P GAIN WILD-TYPE                       3
D20V3, multiclass
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4    7
  20P GAIN WILD-TYPE    6   17
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 4                  6
  YES                7                 17
D20V5, continuous
D20V6, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  3 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-FU-A2QG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
D20V7, continuous
D20V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6    4
  20P GAIN WILD-TYPE   14    5
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                6                 14
  MX                4                  5
D20V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    5
  20P GAIN WILD-TYPE   14    6
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                5                 14
  N1                5                  6
D20V10, continuous
D20V11, continuous

Clustering(21) Variable = 20q gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    9  3
  20Q GAIN WILD-TYPE 18  3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                 21 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                  3 
$`20Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-EA-A1QT TCGA-EA-A3HQ 
       30.41        35.61         2.43        40.93         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3NI TCGA-HM-A3JK 
        1.32         0.82         1.22         2.17         1.45         5.52 

$`20Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A2LY 
       49.48       177.04         5.46        67.46        53.13        78.31 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       70.85        42.38        36.76         2.66        69.93        95.08 
TCGA-DS-A3LQ TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG 
        6.02         0.62         5.85         6.94         1.22         0.99 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        0.07         1.02        25.41 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             40.93             177.04 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             1.955             25.410 
[1] "0.3 - 40.9 (2.0)"   "0.1 - 177.0 (25.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
[1] "hr=" "8.5"
D21V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                  9
  20Q GAIN WILD-TYPE                               18
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20Q GAIN MUTATED                                     1
  20Q GAIN WILD-TYPE                                   0
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                         2
  20Q GAIN WILD-TYPE                       4
D21V3, multiclass
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    8
  20Q GAIN WILD-TYPE    6   16
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 4                  6
  YES                8                 16
D21V5, continuous
D21V6, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-DS-A3LQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG 
"20Q GAIN WILD-TYPE" 
D21V7, continuous
D21V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    4
  20Q GAIN WILD-TYPE   14    5
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                6                 14
  MX                4                  5
D21V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    4
  20Q GAIN WILD-TYPE   13    7
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                6                 13
  N1                4                  7
D21V10, continuous
D21V11, continuous

Clustering(22) Variable = 21q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 25  5
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 30 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  5 
$`21Q GAIN MUTATED`
TCGA-C5-A1MI TCGA-EA-A3HQ TCGA-HM-A3JK 
       35.61         1.74         5.52 

$`21Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HR 
        2.66        69.93        95.08         6.02         0.26         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.82         0.62         5.85         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        0.99         2.17         0.07         1.02         1.45        25.41 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.74               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             35.61             177.04 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             5.520              5.935 
[1] "1.7 - 35.6 (5.5)"  "0.1 - 177.0 (5.9)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
[1] "hr=" "4.8"
D22V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                  2
  21Q GAIN WILD-TYPE                               25
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q GAIN MUTATED                                     0
  21Q GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                         1
  21Q GAIN WILD-TYPE                       5
D22V3, multiclass
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE    8   23
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 2                  8
  YES                1                 23
D22V5, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  9 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D22V6, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-DS-A3LQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG 
"21Q GAIN WILD-TYPE" 
D22V7, continuous
D22V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   18    8
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                2                 18
  MX                1                  8
D22V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    2
  21Q GAIN WILD-TYPE   18    9
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                1                 18
  N1                2                  9
D22V10, continuous
D22V11, continuous

Clustering(23) Variable = 22q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    4  0
  22Q GAIN WILD-TYPE 23  6
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                 29 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  6 
$`22Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A2LY TCGA-DS-A3LQ TCGA-FU-A3NI 
       30.41        78.31         6.02         1.45 

$`22Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48       177.04         5.46        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        40.93        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       69.93        95.08         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.62         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02        25.41         5.52 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.45               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             78.31             177.04 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            18.215              5.520 
[1] "1.4 - 78.3 (18.2)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr="     "2.2e+08"
D23V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                  3
  22Q GAIN WILD-TYPE                               24
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  22Q GAIN MUTATED                                     0
  22Q GAIN WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                         2
  22Q GAIN WILD-TYPE                       4
D23V3, multiclass
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    3
  22Q GAIN WILD-TYPE    8   21
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 2                  8
  YES                3                 21
D23V5, continuous
D23V6, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" 
D23V7, continuous
D23V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE   17    8
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                3                 17
  MX                1                  8
D23V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    2
  22Q GAIN WILD-TYPE   17    9
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                2                 17
  N1                2                  9
D23V10, continuous
D23V11, continuous

Clustering(24) Variable = 3p loss mutation analysis
D24V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    6  3
  3P LOSS WILD-TYPE 21  3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                24 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                 3 
$`3P LOSS MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM TCGA-EA-A3HS 
        5.46        40.93        70.85        36.76        69.93         0.82 
TCGA-EX-A1H5 TCGA-FU-A3HY TCGA-HG-A2PA 
        5.85         0.07        25.41 

$`3P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41       177.04        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ 
        2.43        78.31        42.38         2.66        95.08         6.02 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23K 
        0.26         1.74         1.32         0.62         6.94         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HM-A3JK 
        1.22         0.99         2.17         1.02         1.45         5.52 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.26 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            70.85            177.04 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            25.41              4.09 
[1] "0.1 - 70.8 (25.4)" "0.3 - 177.0 (4.1)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-HM-A3JK 
"3P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-HM-A3JK 
"3P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-HM-A3JK 
"3P LOSS WILD-TYPE" 
[1] "hr=" "2"  
D24V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                  8
  3P LOSS WILD-TYPE                               19
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                     0                       1
  3P LOSS WILD-TYPE                                   1                       5
D24V3, multiclass
D24V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    6
  3P LOSS WILD-TYPE    7   18
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                3                 7
  YES               6                18
D24V5, continuous
D24V6, continuous
D24V7, continuous
D24V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    2
  3P LOSS WILD-TYPE   15    7
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               5                15
  MX               2                 7
D24V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    4
  3P LOSS WILD-TYPE   16    7
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               3                16
  N1               4                 7
D24V10, continuous
D24V11, continuous

Clustering(25) Variable = 4p loss mutation analysis
D25V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   11  3
  4P LOSS WILD-TYPE 16  3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14                19 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                 3 
$`4P LOSS MUTATED`
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-DS-A0VK 
      177.04         5.46        53.13        35.61        70.85        36.76 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EX-A1H5 TCGA-FU-A23L 
        2.66        95.08         1.32         0.82         5.85         1.22 
TCGA-FU-A3HY TCGA-FU-A3NI 
        0.07         1.45 

$`4P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY 
       49.48        30.41        67.46         2.43        40.93        78.31 
TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HT 
       42.38        69.93         6.02         0.26         1.74         0.62 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-HG-A2PA 
        6.94         1.22         0.99         2.17         1.02        25.41 
TCGA-HM-A3JK 
        5.52 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           177.04             78.31 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            5.655             6.020 
[1] "0.1 - 177.0 (5.7)" "0.3 - 78.3 (6.0)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D25V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                 12
  4P LOSS WILD-TYPE                               15
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                     0                       2
  4P LOSS WILD-TYPE                                   1                       4
D25V3, multiclass
D25V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5    9
  4P LOSS WILD-TYPE    5   15
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                5                 5
  YES               9                15
D25V5, continuous
D25V6, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-DS-A3LQ        TCGA-FU-A2QG        TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D25V7, continuous
D25V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7    6
  4P LOSS WILD-TYPE   13    3
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               7                13
  MX               6                 3
D25V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    5
  4P LOSS WILD-TYPE   11    6
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               8                11
  N1               5                 6
D25V10, continuous
D25V11, continuous

Clustering(26) Variable = 4q loss mutation analysis
D26V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  2
  4Q LOSS WILD-TYPE 24  4
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                28 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                 4 
$`4Q LOSS MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-EX-A1H5 TCGA-FU-A3NI 
        5.46        35.61        70.85         5.85         1.45 

$`4Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        30.41       177.04        67.46        53.13         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.93        78.31        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       95.08         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        0.62         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02        25.41         5.52 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.45              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            70.85            177.04 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             5.85              5.77 
[1] "1.4 - 70.8 (5.8)"  "0.1 - 177.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D26V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                  4
  4Q LOSS WILD-TYPE                               23
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                     0                       1
  4Q LOSS WILD-TYPE                                   1                       5
D26V3, multiclass
D26V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3    2
  4Q LOSS WILD-TYPE    7   22
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                3                 7
  YES               2                22
D26V5, continuous
D26V6, continuous
D26V7, continuous
D26V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    2
  4Q LOSS WILD-TYPE   18    7
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               2                18
  MX               2                 7
D26V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   18    8
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               1                18
  N1               3                 8
D26V10, continuous
D26V11, continuous

Clustering(27) Variable = 5q loss mutation analysis
D27V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    7  3
  5Q LOSS WILD-TYPE 20  3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                23 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                 3 
$`5Q LOSS MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        5.46        35.61        70.85        36.76         2.66        69.93 
TCGA-EA-A1QT TCGA-FU-A23L TCGA-FU-A2QG TCGA-HG-A2PA 
        0.26         1.22         0.99        25.41 

$`5Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        30.41       177.04        67.46        53.13         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ 
       40.93        78.31        42.38        95.08         6.02         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K 
        1.32         0.82         0.62         5.85         6.94         1.22 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HM-A3JK 
        2.17         0.07         1.02         1.45         5.52 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.26              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            70.85            177.04 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           15.435             5.850 
[1] "0.3 - 70.8 (15.4)" "0.1 - 177.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" 
[1] "hr=" "2.4"
D27V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                 10
  5Q LOSS WILD-TYPE                               17
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                     0                       0
  5Q LOSS WILD-TYPE                                   1                       6
D27V3, multiclass
D27V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    8
  5Q LOSS WILD-TYPE    8   16
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                2                 8
  YES               8                16
D27V5, continuous
D27V6, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-DS-A3LQ        TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D27V7, continuous
D27V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    1
  5Q LOSS WILD-TYPE   13    8
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               7                13
  MX               1                 8
D27V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6    3
  5Q LOSS WILD-TYPE   13    8
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               6                13
  N1               3                 8
D27V10, continuous
D27V11, continuous

Clustering(28) Variable = 7p loss mutation analysis
D28V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    3  1
  7P LOSS WILD-TYPE 24  5
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                29 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                 5 
$`7P LOSS MUTATED`
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-EX-A1H5 
       53.13        35.61        70.85         5.85 

$`7P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MK 
       49.48        30.41       177.04         5.46        67.46         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.93        78.31        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       95.08         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        0.62         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             5.85              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            70.85            177.04 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            44.37              5.46 
[1] "5.8 - 70.8 (44.4)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D28V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                  4
  7P LOSS WILD-TYPE                               23
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                     0                       0
  7P LOSS WILD-TYPE                                   1                       6
D28V3, multiclass
D28V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    1
  7P LOSS WILD-TYPE    7   23
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                3                 7
  YES               1                23
D28V5, continuous
D28V6, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-DS-A3LQ        TCGA-FU-A2QG        TCGA-HM-A3JK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D28V7, continuous
D28V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    2
  7P LOSS WILD-TYPE   18    7
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               2                18
  MX               2                 7
D28V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    2
  7P LOSS WILD-TYPE   17    9
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               2                17
  N1               2                 9
D28V10, continuous
D28V11, continuous

Clustering(29) Variable = 7q loss mutation analysis
D29V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    2  2
  7Q LOSS WILD-TYPE 25  4
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                29 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                 4 
$`7Q LOSS MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-EX-A1H5 TCGA-FU-A2QG 
        5.46        35.61         5.85         0.99 

$`7Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        30.41       177.04        67.46        53.13         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       40.93        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
        0.82         0.62         6.94         1.22         1.22         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.99              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            35.61            177.04 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            5.655             6.020 
[1] "1.0 - 35.6 (5.7)"  "0.1 - 177.0 (6.0)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q LOSS WILD-TYPE" 
[1] "hr=" "14" 
D29V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                  4
  7Q LOSS WILD-TYPE                               23
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                     0                       0
  7Q LOSS WILD-TYPE                                   1                       6
D29V3, multiclass
D29V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE    7   23
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                3                 7
  YES               1                23
D29V5, continuous
D29V6, continuous
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                 4 
       TCGA-BI-A0VR        TCGA-C5-A1MF        TCGA-DS-A3LQ        TCGA-HM-A3JK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D29V7, continuous
D29V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    1
  7Q LOSS WILD-TYPE   19    8
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               1                19
  MX               1                 8
D29V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE   18    9
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               1                18
  N1               2                 9
D29V10, continuous
D29V11, continuous

Clustering(30) Variable = 8p loss mutation analysis
D30V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    6  3
  8P LOSS WILD-TYPE 21  3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                24 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                 3 
$`8P LOSS MUTATED`
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT 
        2.43        40.93        78.31        36.76        95.08         0.26 
TCGA-EA-A3HR TCGA-FU-A23K TCGA-FU-A3NI 
        1.32         1.22         1.45 

$`8P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       35.61        70.85        42.38         2.66        69.93         6.02 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L 
        1.74         0.82         0.62         5.85         6.94         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        0.99         2.17         0.07         1.02        25.41         5.52 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            95.08            177.04 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            2.430             5.935 
[1] "0.3 - 95.1 (2.4)"  "0.1 - 177.0 (5.9)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"8P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"8P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"8P LOSS WILD-TYPE" 
[1] "hr=" "2.4"
D30V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                  9
  8P LOSS WILD-TYPE                               18
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                     0                       1
  8P LOSS WILD-TYPE                                   1                       5
D30V3, multiclass
D30V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    6
  8P LOSS WILD-TYPE    6   18
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                 6
  YES               6                18
D30V5, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 9 
       TCGA-BI-A0VR        TCGA-C5-A1BN        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3HY 
"8P LOSS WILD-TYPE" 
D30V6, continuous
D30V7, continuous
D30V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    2
  8P LOSS WILD-TYPE   15    7
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               5                15
  MX               2                 7
D30V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    3
  8P LOSS WILD-TYPE   15    8
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               4                15
  N1               3                 8
D30V10, continuous
D30V11, continuous

Clustering(31) Variable = 9p loss mutation analysis
D31V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    2  2
  9P LOSS WILD-TYPE 25  4
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 4 
$`9P LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-EA-A1QT TCGA-EA-A3HR 
       35.61        40.93         0.26         1.32 

$`9P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       69.93        95.08         6.02         1.74         0.82         0.62 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.26              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            40.93            177.04 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           18.465             5.850 
[1] "0.3 - 40.9 (18.5)" "0.1 - 177.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9P LOSS WILD-TYPE" 
[1] "hr=" "5.4"
D31V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                  4
  9P LOSS WILD-TYPE                               23
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                     0                       0
  9P LOSS WILD-TYPE                                   1                       6
D31V3, multiclass
D31V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    2
  9P LOSS WILD-TYPE    8   22
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                2                 8
  YES               2                22
D31V5, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 8 
       TCGA-BI-A0VR        TCGA-C5-A1BN        TCGA-C5-A1MF        TCGA-DR-A0ZM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
D31V6, continuous
D31V7, continuous
D31V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3    0
  9P LOSS WILD-TYPE   17    9
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               3                17
  MX               0                 9
D31V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    1
  9P LOSS WILD-TYPE   17   10
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               2                17
  N1               1                10
D31V10, continuous
D31V11, continuous

Clustering(32) Variable = 9q loss mutation analysis
D32V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    2  1
  9Q LOSS WILD-TYPE 25  5
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 5 
$`9Q LOSS MUTATED`
TCGA-C5-A1MI TCGA-EA-A1QT TCGA-EA-A3HR 
       35.61         0.26         1.32 

$`9Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HS 
        2.66        69.93        95.08         6.02         1.74         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.62         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02         1.45        25.41         5.52 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.26              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            35.61            177.04 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            1.320             5.935 
[1] "0.3 - 35.6 (1.3)"  "0.1 - 177.0 (5.9)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BK        TCGA-C5-A1BN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EX-A1H5        TCGA-EX-A3L1 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-HG-A2PA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" 
[1] "hr=" "7.8"
D32V2, continuous
                   vv
clus                CERVICAL SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                  3
  9Q LOSS WILD-TYPE                               24
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                     0                       0
  9Q LOSS WILD-TYPE                                   1                       6
D32V3, multiclass
D32V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1    2
  9Q LOSS WILD-TYPE    9   22
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 9
  YES               2                22
D32V5, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 9 
       TCGA-BI-A0VR        TCGA-C5-A1BN        TCGA-C5-A1MF        TCGA-C5-A1MN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY 
"9Q LOSS WILD-TYPE" 
D32V6, continuous
D32V7, continuous
D32V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    0
  9Q LOSS WILD-TYPE   17    9
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               3                17
  MX               0                 9
D32V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2    1
  9Q LOSS WILD-TYPE   17   10
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               2                17
  N1               1                10
D32V10, continuous
D32V11, continuous

Clustering(33) Variable = 10p loss mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    4  2
  10P LOSS WILD-TYPE 23  4
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 27 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  4 
$`10P LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-HM-A3JK 
       35.61        40.93         5.85         1.22         0.99         5.52 

$`10P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        0.82         0.62         6.94         1.22         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        1.02         1.45        25.41 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.99               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             40.93             177.04 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             5.685              6.020 
[1] "1.0 - 40.9 (5.7)"  "0.1 - 177.0 (6.0)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
[1] "hr=" "3.9"
D33V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                  6
  10P LOSS WILD-TYPE                               21
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P LOSS MUTATED                                     0
  10P LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                         1
  10P LOSS WILD-TYPE                       5
D33V3, multiclass
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    3
  10P LOSS WILD-TYPE    6   21
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 4                  6
  YES                3                 21
D33V5, continuous
D33V6, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  3 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-DS-A3LQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
D33V7, continuous
D33V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    3
  10P LOSS WILD-TYPE   19    6
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                1                 19
  MX                3                  6
D33V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    4
  10P LOSS WILD-TYPE   18    7
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                1                 18
  N1                4                  7
D33V10, continuous
D33V11, continuous

Clustering(34) Variable = 10q loss mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    4  2
  10Q LOSS WILD-TYPE 23  4
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                 27 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  4 
$`10Q LOSS MUTATED`
TCGA-C5-A1MI TCGA-DS-A0VK TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-HM-A3JK 
       35.61        36.76         5.85         1.22         0.99         5.52 

$`10Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
        2.43        40.93        78.31        70.85        42.38         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        0.82         0.62         6.94         1.22         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        1.02         1.45        25.41 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.99               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             36.76             177.04 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             5.685              6.020 
[1] "1.0 - 36.8 (5.7)"  "0.1 - 177.0 (6.0)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
[1] "hr=" "5.3"
D34V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                  5
  10Q LOSS WILD-TYPE                               22
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10Q LOSS MUTATED                                     0
  10Q LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                         1
  10Q LOSS WILD-TYPE                       5
D34V3, multiclass
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    3
  10Q LOSS WILD-TYPE    7   21
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 3                  7
  YES                3                 21
D34V5, continuous
D34V6, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  3 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-DS-A3LQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D34V7, continuous
D34V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2    3
  10Q LOSS WILD-TYPE   18    6
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                2                 18
  MX                3                  6
D34V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    5
  10Q LOSS WILD-TYPE   18    6
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                1                 18
  N1                5                  6
D34V10, continuous
D34V11, continuous

Clustering(35) Variable = 11p loss mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    6  1
  11P LOSS WILD-TYPE 21  5
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 26 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  5 
$`11P LOSS MUTATED`
TCGA-C5-A1BK TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EX-A1H5 TCGA-FU-A23L 
      177.04        35.61        70.85        95.08         5.85         1.22 
TCGA-FU-A3NI 
        1.45 

$`11P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        30.41         5.46        67.46        53.13         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.93        78.31        42.38        36.76         2.66        69.93 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        6.02         0.26         1.74         1.32         0.82         0.62 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.94         1.22         0.99         2.17         0.07         1.02 
TCGA-HG-A2PA TCGA-HM-A3JK 
       25.41         5.52 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.22               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            177.04              78.31 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             35.61               5.49 
[1] "1.2 - 177.0 (35.6)" "0.1 - 78.3 (5.5)"  
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "2.4"
D35V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                  6
  11P LOSS WILD-TYPE                               21
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11P LOSS MUTATED                                     0
  11P LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                         1
  11P LOSS WILD-TYPE                       5
D35V3, multiclass
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    4
  11P LOSS WILD-TYPE    7   20
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 3                  7
  YES                4                 20
D35V5, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                  8 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-DR-A0ZM         TCGA-FU-A2QG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D35V6, continuous
D35V7, continuous
D35V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    4
  11P LOSS WILD-TYPE   17    5
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                3                 17
  MX                4                  5
D35V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    3
  11P LOSS WILD-TYPE   15    8
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                4                 15
  N1                3                  8
D35V10, continuous
D35V11, continuous

Clustering(36) Variable = 11q loss mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    5  1
  11Q LOSS WILD-TYPE 22  5
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  5 
$`11Q LOSS MUTATED`
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A3NI 
       53.13        35.61        95.08         0.26         5.85         1.45 

$`11Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MK 
       49.48        30.41       177.04         5.46        67.46         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       40.93        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       69.93         6.02         1.74         1.32         0.82         0.62 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02        25.41         5.52 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.26               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             95.08             177.04 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             20.73               5.52 
[1] "0.3 - 95.1 (20.7)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D36V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                  6
  11Q LOSS WILD-TYPE                               21
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11Q LOSS MUTATED                                     0
  11Q LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                         1
  11Q LOSS WILD-TYPE                       5
D36V3, multiclass
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    3
  11Q LOSS WILD-TYPE    6   21
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 4                  6
  YES                3                 21
D36V5, continuous
D36V6, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-DS-A3LQ         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK 
"11Q LOSS WILD-TYPE" 
D36V7, continuous
D36V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    3
  11Q LOSS WILD-TYPE   17    6
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                3                 17
  MX                3                  6
D36V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    3
  11Q LOSS WILD-TYPE   16    8
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                3                 16
  N1                3                  8
D36V10, continuous
D36V11, continuous

Clustering(37) Variable = 12p loss mutation analysis
D37V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    4  2
  12P LOSS WILD-TYPE 23  4
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 27 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                  4 
$`12P LOSS MUTATED`
TCGA-C5-A1BK TCGA-C5-A1MN TCGA-DS-A0VK TCGA-DS-A0VL TCGA-EA-A1QT TCGA-FU-A2QG 
      177.04        40.93        36.76         2.66         0.26         0.99 

$`12P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41         5.46        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A0VN 
        2.43        78.31        70.85        42.38        69.93        95.08 
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 
        6.02         1.74         1.32         0.82         0.62         5.85 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.94         1.22         1.22         2.17         0.07         1.02 
TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        1.45        25.41         5.52 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.26               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            177.04              95.08 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             19.71               5.85 
[1] "0.3 - 177.0 (19.7)" "0.1 - 95.1 (5.8)"  
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D37V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                  6
  12P LOSS WILD-TYPE                               21
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P LOSS MUTATED                                     0
  12P LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                         0
  12P LOSS WILD-TYPE                       6
D37V3, multiclass
D37V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    5
  12P LOSS WILD-TYPE    9   19
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  9
  YES                5                 19
D37V5, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                  8 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D37V6, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-DS-A3LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" 
D37V7, continuous
D37V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    1
  12P LOSS WILD-TYPE   17    8
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                3                 17
  MX                1                  8
D37V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    1
  12P LOSS WILD-TYPE   15   10
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                4                 15
  N1                1                 10
D37V10, continuous
D37V11, continuous

Clustering(38) Variable = 13q loss mutation analysis
D38V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    7  0
  13Q LOSS WILD-TYPE 20  6
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                 26 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  6 
$`13Q LOSS MUTATED`
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI 
       95.08         6.02         0.26         5.85         1.22         1.45 
TCGA-HG-A2PA 
       25.41 

$`13Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       36.76         2.66        69.93         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        0.62         6.94         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-HM-A3JK 
        1.02         5.52 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.26               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             95.08             177.04 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              5.85               6.23 
[1] "0.3 - 95.1 (5.8)"  "0.1 - 177.0 (6.2)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
[1] "hr="     "2.4e+08"
D38V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                  6
  13Q LOSS WILD-TYPE                               21
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                         2
  13Q LOSS WILD-TYPE                       4
D38V3, multiclass
D38V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    5
  13Q LOSS WILD-TYPE    7   19
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 3                  7
  YES                5                 19
D38V5, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MN         TCGA-DR-A0ZM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D38V6, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  4 
        TCGA-BI-A0VR         TCGA-C5-A1MF         TCGA-FU-A2QG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK 
"13Q LOSS WILD-TYPE" 
D38V7, continuous
D38V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    3
  13Q LOSS WILD-TYPE   16    6
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                4                 16
  MX                3                  6
D38V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    3
  13Q LOSS WILD-TYPE   15    8
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                4                 15
  N1                3                  8
D38V10, continuous
D38V11, continuous

Clustering(39) Variable = 17p loss mutation analysis
D39V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    6  4
  17P LOSS WILD-TYPE 21  2
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                  2 
$`17P LOSS MUTATED`
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL 
        5.46        67.46        40.93        70.85        36.76         2.66 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A3NI 
       95.08         0.26         5.85         1.45 

$`17P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK 
       49.48        30.41       177.04        53.13        35.61         2.43 
TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR 
       78.31        42.38        69.93         6.02         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.82         0.62         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02        25.41         5.52 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             95.08             177.04 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            21.305              5.520 
[1] "0.3 - 95.1 (21.3)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D39V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                  9
  17P LOSS WILD-TYPE                               18
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17P LOSS MUTATED                                     0
  17P LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                         1
  17P LOSS WILD-TYPE                       5
D39V3, multiclass
D39V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    6
  17P LOSS WILD-TYPE    6   18
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                  6
  YES                6                 18
D39V5, continuous
D39V6, continuous
D39V7, continuous
D39V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    2
  17P LOSS WILD-TYPE   14    7
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                6                 14
  MX                2                  7
D39V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    3
  17P LOSS WILD-TYPE   14    8
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                5                 14
  N1                3                  8
D39V10, continuous
D39V11, continuous

Clustering(40) Variable = 17q loss mutation analysis
D40V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    2  1
  17Q LOSS WILD-TYPE 25  5
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 30 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                  5 
$`17Q LOSS MUTATED`
TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT 
       36.76        95.08         0.26 

$`17Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        2.66        69.93         6.02         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.62         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02         1.45        25.41         5.52 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.26               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             95.08             177.04 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            36.760              5.685 
[1] "0.3 - 95.1 (36.8)" "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D40V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                  3
  17Q LOSS WILD-TYPE                               24
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                         0
  17Q LOSS WILD-TYPE                       6
D40V3, multiclass
D40V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE    9   22
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  9
  YES                2                 22
D40V5, continuous
D40V6, continuous
D40V7, continuous
D40V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    0
  17Q LOSS WILD-TYPE   17    9
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                3                 17
  MX                0                  9
D40V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    1
  17Q LOSS WILD-TYPE   17   10
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                2                 17
  N1                1                 10
D40V10, continuous
D40V11, continuous

Clustering(41) Variable = 18p loss mutation analysis
D41V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    4  2
  18P LOSS WILD-TYPE 23  4
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 27 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  4 
$`18P LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DS-A0VN TCGA-EA-A1QT TCGA-FU-A3EO 
       35.61        40.93        78.31        95.08         0.26         2.17 

$`18P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        2.43        70.85        42.38        36.76         2.66        69.93 
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 
        6.02         1.74         1.32         0.82         0.62         5.85 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.94         1.22         1.22         0.99         0.07         1.02 
TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        1.45        25.41         5.52 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.26               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             95.08             177.04 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             38.27               5.52 
[1] "0.3 - 95.1 (38.3)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D41V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                  5
  18P LOSS WILD-TYPE                               22
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P LOSS MUTATED                                     1
  18P LOSS WILD-TYPE                                   0
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                         0
  18P LOSS WILD-TYPE                       6
D41V3, multiclass
D41V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    2
  18P LOSS WILD-TYPE    6   22
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 4                  6
  YES                2                 22
D41V5, continuous
D41V6, continuous
D41V7, continuous
D41V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    1
  18P LOSS WILD-TYPE   16    8
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                4                 16
  MX                1                  8
D41V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    1
  18P LOSS WILD-TYPE   15   10
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                4                 15
  N1                1                 10
D41V10, continuous
D41V11, continuous

Clustering(42) Variable = 18q loss mutation analysis
D42V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    5  2
  18Q LOSS WILD-TYPE 22  4
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 26 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  4 
$`18Q LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QT 
       35.61        40.93        78.31        70.85        95.08         0.26 
TCGA-FU-A3EO 
        2.17 

$`18Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
        2.43        42.38        36.76         2.66        69.93         6.02 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 
        1.74         1.32         0.82         0.62         5.85         6.94 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22         1.22         0.99         0.07         1.02         1.45 
TCGA-HG-A2PA TCGA-HM-A3JK 
       25.41         5.52 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.26               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             95.08             177.04 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             40.93               5.49 
[1] "0.3 - 95.1 (40.9)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D42V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                  6
  18Q LOSS WILD-TYPE                               21
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18Q LOSS MUTATED                                     1
  18Q LOSS WILD-TYPE                                   0
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                         0
  18Q LOSS WILD-TYPE                       6
D42V3, multiclass
D42V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    3
  18Q LOSS WILD-TYPE    6   21
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 4                  6
  YES                3                 21
D42V5, continuous
D42V6, continuous
D42V7, continuous
D42V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    1
  18Q LOSS WILD-TYPE   15    8
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                5                 15
  MX                1                  8
D42V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    1
  18Q LOSS WILD-TYPE   14   10
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                5                 14
  N1                1                 10
D42V10, continuous
D42V11, continuous

Clustering(43) Variable = 19p loss mutation analysis
D43V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    1  2
  19P LOSS WILD-TYPE 26  4
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 30 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                  4 
$`19P LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DS-A0VN 
       35.61        40.93        95.08 

$`19P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       69.93         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.62         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02         1.45        25.41         5.52 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             35.61               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             95.08             177.04 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             40.93               5.49 
[1] "35.6 - 95.1 (40.9)" "0.1 - 177.0 (5.5)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D43V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                  4
  19P LOSS WILD-TYPE                               23
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19P LOSS MUTATED                                     0
  19P LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                         0
  19P LOSS WILD-TYPE                       6
D43V3, multiclass
D43V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    1
  19P LOSS WILD-TYPE    7   23
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 3                  7
  YES                1                 23
D43V5, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                  8 
        TCGA-BI-A0VR         TCGA-C5-A1BN         TCGA-C5-A1MF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-EX-A1H5         TCGA-FU-A2QG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D43V6, continuous
D43V7, continuous
D43V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    0
  19P LOSS WILD-TYPE   18    9
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                2                 18
  MX                0                  9
D43V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    1
  19P LOSS WILD-TYPE   18   10
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                1                 18
  N1                1                 10
D43V10, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 28 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1MF         TCGA-C5-A2LY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A3LQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EX-A1H5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-HG-A2PA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" 
D43V11, continuous

Clustering(44) Variable = 21q loss mutation analysis
D44V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    6  0
  21Q LOSS WILD-TYPE 21  6
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 27 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  6 
$`21Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-FU-A23L TCGA-FU-A3NI 
       30.41        70.85         2.66         1.32         1.22         1.45 

$`21Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48       177.04         5.46        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
        2.43        40.93        78.31        42.38        36.76        69.93 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       95.08         6.02         0.26         1.74         0.82         0.62 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        5.85         6.94         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02        25.41         5.52 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.22               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             70.85             177.04 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             2.055              6.020 
[1] "1.2 - 70.8 (2.1)"  "0.1 - 177.0 (6.0)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1M5         TCGA-C5-A1MF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A1QT 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-HG-A2PA         TCGA-HM-A3JK 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr="     "2.2e+08"
D44V2, continuous
                    vv
clus                 CERVICAL SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                  5
  21Q LOSS WILD-TYPE                               22
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q LOSS MUTATED                                     0
  21Q LOSS WILD-TYPE                                   1
                    vv
clus                 SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                         1
  21Q LOSS WILD-TYPE                       5
D44V3, multiclass
D44V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    6
  21Q LOSS WILD-TYPE   10   18
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 0                 10
  YES                6                 18
D44V5, continuous
D44V6, continuous
D44V7, continuous
D44V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    2
  21Q LOSS WILD-TYPE   16    7
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                4                 16
  MX                2                  7
D44V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    1
  21Q LOSS WILD-TYPE   14   10
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                5                 14
  N1                1                 10
D44V10, continuous
D44V11, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                     "HISTOLOGICAL.TYPE" 
                                      V4 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V5 
                 "NUMBERPACKYEARSSMOKED" 
                                      V6 
                    "STOPPEDSMOKINGYEAR" 
                                      V7 
        "TOBACCOSMOKINGHISTORYINDICATOR" 
                                      V8 
                    "DISTANT.METASTASIS" 
                                      V9 
                 "LYMPH.NODE.METASTASIS" 
                                     V10 
                 "NUMBER.OF.LYMPH.NODES" 
                                     V11 
                       "TUMOR.STAGECODE" 
> q(save="no")
