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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/4466671/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/4434596/KICH-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KICH-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KICH-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/4434596/KICH-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/4466671/transformed.cor.cli.txt"

nPatients in clinical file=64, in cluster file=66, common to both=64
[1]  2 64
[1] "AMP PEAK 1(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           17                            47 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           17                            47 
[1] "AMP PEAK 2(15Q22.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            21                             43 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            21                             43 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "NEOPLASM.DISEASESTAGE"           
 [7] "PATHOLOGY.T.STAGE"                "PATHOLOGY.N.STAGE"               
 [9] "PATHOLOGY.M.STAGE"                "DCCUPLOADDATE"                   
[11] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
[13] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[15] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[17] "YEAROFTOBACCOSMOKINGONSET"        "BATCHNUMBER"                     

Input Data has 18 rows and 64 columns.

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

$Table
vv
T1 T2 T3 T4 
21 23 18  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


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

$Table
vv
N0 N1 N2 
40  3  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 40

$Class1_nSamples
[1] 5

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


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

Clustering(1) Variable = AMP PEAK 1(8Q11.23) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 1(8Q11.23) MUTATED   13  3
  AMP PEAK 1(8Q11.23) WILD-TYPE 43  4
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           16                            47 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                            3                             4 
$`AMP PEAK 1(8Q11.23) MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
       98.93        28.08        24.79        62.33       151.92        37.08 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.52         0.56        52.27        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       74.93        80.38        87.78        86.07 

$`AMP PEAK 1(8Q11.23) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.18       137.06       102.77        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.30        96.95        92.55        30.21        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.53        66.54        73.91        59.67        28.80        54.71 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
        8.12        32.68        13.15        35.57       123.12        51.02 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
       31.33       114.18        87.91        25.48        65.19        72.69 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       67.82        23.41         2.50        36.95        89.65        20.91 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       75.72        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        77.85        57.17        61.58        63.91 

  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                         0.56                          2.50 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                       151.92                        137.06 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                       44.675                        66.540 
[1] "0.6 - 151.9 (44.7)" "2.5 - 137.1 (66.5)"
                   TCGA-KL-8323                    TCGA-KL-8326 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8327                    TCGA-KL-8328 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8329                    TCGA-KL-8330 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8331                    TCGA-KL-8332 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8333                    TCGA-KL-8334 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8335                    TCGA-KL-8336 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8337                    TCGA-KL-8338 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8339                    TCGA-KL-8340 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8341                    TCGA-KL-8342 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8343                    TCGA-KL-8344 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8345                    TCGA-KL-8346 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KM-8438                    TCGA-KM-8439 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8440                    TCGA-KM-8441 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8442                    TCGA-KM-8443 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KM-8476                    TCGA-KM-8477 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8639                    TCGA-KN-8418 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8419                    TCGA-KN-8421 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8422                    TCGA-KN-8423 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KN-8424                    TCGA-KN-8425 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8426                    TCGA-KN-8427 
  "AMP PEAK 1(8Q11.23) MUTATED"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KN-8428                    TCGA-KN-8429 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8431                    TCGA-KN-8432 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8433                    TCGA-KN-8434 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8435                    TCGA-KN-8436 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8437                    TCGA-KO-8403 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8404                    TCGA-KO-8405 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KO-8406                    TCGA-KO-8407 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8408                    TCGA-KO-8409 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KO-8410                    TCGA-KO-8411 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8413                    TCGA-KO-8414 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8415                    TCGA-KO-8416 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8417 
"AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8323                    TCGA-KL-8326 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8327                    TCGA-KL-8328 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8329                    TCGA-KL-8330 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8331                    TCGA-KL-8332 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8333                    TCGA-KL-8334 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8335                    TCGA-KL-8336 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8337                    TCGA-KL-8338 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8339                    TCGA-KL-8340 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8341                    TCGA-KL-8342 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8343                    TCGA-KL-8344 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8345                    TCGA-KL-8346 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KM-8438                    TCGA-KM-8439 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8440                    TCGA-KM-8441 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8442                    TCGA-KM-8443 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KM-8476                    TCGA-KM-8477 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8639                    TCGA-KN-8418 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8419                    TCGA-KN-8421 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8422                    TCGA-KN-8423 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KN-8424                    TCGA-KN-8425 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8426                    TCGA-KN-8427 
  "AMP PEAK 1(8Q11.23) MUTATED"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KN-8428                    TCGA-KN-8429 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8431                    TCGA-KN-8432 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8433                    TCGA-KN-8434 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8435                    TCGA-KN-8436 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8437                    TCGA-KO-8403 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8404                    TCGA-KO-8405 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KO-8406                    TCGA-KO-8407 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8408                    TCGA-KO-8409 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KO-8410                    TCGA-KO-8411 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8413                    TCGA-KO-8414 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8415                    TCGA-KO-8416 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8417 
"AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8323                    TCGA-KL-8326 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8327                    TCGA-KL-8328 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8329                    TCGA-KL-8330 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8331                    TCGA-KL-8332 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8333                    TCGA-KL-8334 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8335                    TCGA-KL-8336 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8337                    TCGA-KL-8338 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8339                    TCGA-KL-8340 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8341                    TCGA-KL-8342 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8343                    TCGA-KL-8344 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KL-8345                    TCGA-KL-8346 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KM-8438                    TCGA-KM-8439 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8440                    TCGA-KM-8441 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8442                    TCGA-KM-8443 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KM-8476                    TCGA-KM-8477 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8639                    TCGA-KN-8418 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8419                    TCGA-KN-8421 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8422                    TCGA-KN-8423 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KN-8424                    TCGA-KN-8425 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8426                    TCGA-KN-8427 
  "AMP PEAK 1(8Q11.23) MUTATED"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KN-8428                    TCGA-KN-8429 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8431                    TCGA-KN-8432 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8433                    TCGA-KN-8434 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8435                    TCGA-KN-8436 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KN-8437                    TCGA-KO-8403 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8404                    TCGA-KO-8405 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KO-8406                    TCGA-KO-8407 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8408                    TCGA-KO-8409 
"AMP PEAK 1(8Q11.23) WILD-TYPE"   "AMP PEAK 1(8Q11.23) MUTATED" 
                   TCGA-KO-8410                    TCGA-KO-8411 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8413                    TCGA-KO-8414 
  "AMP PEAK 1(8Q11.23) MUTATED" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8415                    TCGA-KO-8416 
"AMP PEAK 1(8Q11.23) WILD-TYPE" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KO-8417 
"AMP PEAK 1(8Q11.23) WILD-TYPE" 
[1] "hr=" "2.8"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(8Q11.23) MUTATED         4        7         2        4
  AMP PEAK 1(8Q11.23) WILD-TYPE      17       16        12        2
D1V3, multiclass
           clus
vv          AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  STAGE I                             4                            17
  STAGE II                            7                            16
  STAGE III                           2                            12
  STAGE IV                            4                             2
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK 1(8Q11.23) MUTATED    4  7     6
  AMP PEAK 1(8Q11.23) WILD-TYPE 17 16    14
D1V4, multiclass
       clus
vv      AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  T1                              4                            17
  T2                              7                            16
  T3+T4                           6                            14
                               vv
clus                            N0 N1+N2
  AMP PEAK 1(8Q11.23) MUTATED   12     3
  AMP PEAK 1(8Q11.23) WILD-TYPE 28     2
D1V5, multiclass
       clus
vv      AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  N0                             12                            28
  N1+N2                           3                             2
                               vv
clus                            M0 M1 MX
  AMP PEAK 1(8Q11.23) MUTATED    7  2  2
  AMP PEAK 1(8Q11.23) WILD-TYPE 25  0  7
D1V6, multiclass
    clus
vv   AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  M0                           7                            25
  M1                           2                             0
  MX                           2                             7
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK 1(8Q11.23) MUTATED    4 13
  AMP PEAK 1(8Q11.23) WILD-TYPE 21 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(8Q11.23) MUTATED      4   13
  AMP PEAK 1(8Q11.23) WILD-TYPE   21   26
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  FEMALE                           4                            21
  MALE                            13                            26
D1V8, continuous
D1V9, continuous
D1V10, continuous

Clustering(2) Variable = AMP PEAK 2(15Q22.31) MUTATION ANALYSIS
D2V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 2(15Q22.31) MUTATED   15  5
  AMP PEAK 2(15Q22.31) WILD-TYPE 41  2
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            20                             43 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                             5                              2 
$`AMP PEAK 2(15Q22.31) MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      137.06        98.93        30.21        28.08        24.79        62.33 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
      151.92        37.08        23.47        72.69         3.52        52.27 
TCGA-KN-8433 TCGA-KN-8435 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 
       11.21        89.65        74.93        16.67        80.38        86.07 
TCGA-KO-8414 TCGA-KO-8415 
       77.85        57.17 

$`AMP PEAK 2(15Q22.31) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07       109.18       102.77        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       98.30        96.95        92.55        44.84        86.53        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 
       73.91        59.67        28.80        54.71         8.12        32.68 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       13.15        35.57       123.12        51.02        31.33       114.18 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 
       87.91        25.48        25.91        65.19         0.56        67.82 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       23.41         2.50        36.95        20.91        75.72        76.90 
TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 
       10.68        79.04        92.71        87.78       103.27        61.58 
TCGA-KO-8417 
       63.91 

  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                          3.52                           0.56 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                        151.92                         123.12 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                         59.75                          65.19 
[1] "3.5 - 151.9 (59.8)" "0.6 - 123.1 (65.2)"
                    TCGA-KL-8323                     TCGA-KL-8326 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8327                     TCGA-KL-8328 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8329                     TCGA-KL-8330 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8331                     TCGA-KL-8332 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8333                     TCGA-KL-8334 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8335                     TCGA-KL-8336 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KL-8337                     TCGA-KL-8338 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8339                     TCGA-KL-8340 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8341                     TCGA-KL-8342 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8343                     TCGA-KL-8344 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8345                     TCGA-KL-8346 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KM-8438                     TCGA-KM-8439 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8440                     TCGA-KM-8441 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8442                     TCGA-KM-8443 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KM-8476                     TCGA-KM-8477 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8639                     TCGA-KN-8418 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8419                     TCGA-KN-8421 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8422                     TCGA-KN-8423 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8424                     TCGA-KN-8425 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KN-8426                     TCGA-KN-8427 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8428                     TCGA-KN-8429 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8431                     TCGA-KN-8432 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8433                     TCGA-KN-8434 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8435                     TCGA-KN-8436 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8437                     TCGA-KO-8403 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8404                     TCGA-KO-8405 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8406                     TCGA-KO-8407 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8408                     TCGA-KO-8409 
  "AMP PEAK 2(15Q22.31) MUTATED"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8410                     TCGA-KO-8411 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8413                     TCGA-KO-8414 
  "AMP PEAK 2(15Q22.31) MUTATED"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8415                     TCGA-KO-8416 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8417 
"AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8323                     TCGA-KL-8326 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8327                     TCGA-KL-8328 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8329                     TCGA-KL-8330 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8331                     TCGA-KL-8332 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8333                     TCGA-KL-8334 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8335                     TCGA-KL-8336 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KL-8337                     TCGA-KL-8338 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8339                     TCGA-KL-8340 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8341                     TCGA-KL-8342 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8343                     TCGA-KL-8344 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8345                     TCGA-KL-8346 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KM-8438                     TCGA-KM-8439 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8440                     TCGA-KM-8441 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8442                     TCGA-KM-8443 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KM-8476                     TCGA-KM-8477 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8639                     TCGA-KN-8418 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8419                     TCGA-KN-8421 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8422                     TCGA-KN-8423 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8424                     TCGA-KN-8425 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KN-8426                     TCGA-KN-8427 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8428                     TCGA-KN-8429 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8431                     TCGA-KN-8432 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8433                     TCGA-KN-8434 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8435                     TCGA-KN-8436 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8437                     TCGA-KO-8403 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8404                     TCGA-KO-8405 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8406                     TCGA-KO-8407 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8408                     TCGA-KO-8409 
  "AMP PEAK 2(15Q22.31) MUTATED"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8410                     TCGA-KO-8411 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8413                     TCGA-KO-8414 
  "AMP PEAK 2(15Q22.31) MUTATED"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8415                     TCGA-KO-8416 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8417 
"AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8323                     TCGA-KL-8326 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8327                     TCGA-KL-8328 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8329                     TCGA-KL-8330 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8331                     TCGA-KL-8332 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8333                     TCGA-KL-8334 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8335                     TCGA-KL-8336 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KL-8337                     TCGA-KL-8338 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8339                     TCGA-KL-8340 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8341                     TCGA-KL-8342 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8343                     TCGA-KL-8344 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KL-8345                     TCGA-KL-8346 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KM-8438                     TCGA-KM-8439 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8440                     TCGA-KM-8441 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8442                     TCGA-KM-8443 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KM-8476                     TCGA-KM-8477 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8639                     TCGA-KN-8418 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8419                     TCGA-KN-8421 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8422                     TCGA-KN-8423 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8424                     TCGA-KN-8425 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KN-8426                     TCGA-KN-8427 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8428                     TCGA-KN-8429 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8431                     TCGA-KN-8432 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8433                     TCGA-KN-8434 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8435                     TCGA-KN-8436 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8437                     TCGA-KO-8403 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8404                     TCGA-KO-8405 
"AMP PEAK 2(15Q22.31) WILD-TYPE"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8406                     TCGA-KO-8407 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8408                     TCGA-KO-8409 
  "AMP PEAK 2(15Q22.31) MUTATED"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8410                     TCGA-KO-8411 
"AMP PEAK 2(15Q22.31) WILD-TYPE" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8413                     TCGA-KO-8414 
  "AMP PEAK 2(15Q22.31) MUTATED"   "AMP PEAK 2(15Q22.31) MUTATED" 
                    TCGA-KO-8415                     TCGA-KO-8416 
  "AMP PEAK 2(15Q22.31) MUTATED" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KO-8417 
"AMP PEAK 2(15Q22.31) WILD-TYPE" 
[1] "hr=" "5.6"
D2V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(15Q22.31) MUTATED         5        9         3        4
  AMP PEAK 2(15Q22.31) WILD-TYPE      16       14        11        2
D2V3, multiclass
           clus
vv          AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  STAGE I                              5                             16
  STAGE II                             9                             14
  STAGE III                            3                             11
  STAGE IV                             4                              2
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 2(15Q22.31) MUTATED    5  9     7
  AMP PEAK 2(15Q22.31) WILD-TYPE 16 14    13
D2V4, multiclass
       clus
vv      AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  T1                               5                             16
  T2                               9                             14
  T3+T4                            7                             13
                                vv
clus                             N0 N1+N2
  AMP PEAK 2(15Q22.31) MUTATED   14     4
  AMP PEAK 2(15Q22.31) WILD-TYPE 26     1
D2V5, multiclass
       clus
vv      AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  N0                              14                             26
  N1+N2                            4                              1
                                vv
clus                             M0 M1 MX
  AMP PEAK 2(15Q22.31) MUTATED   10  2  2
  AMP PEAK 2(15Q22.31) WILD-TYPE 22  0  7
D2V6, multiclass
    clus
vv   AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  M0                           10                             22
  M1                            2                              0
  MX                            2                              7
D2V7, binary
                                cls
clus                              0  1
  AMP PEAK 2(15Q22.31) MUTATED    7 14
  AMP PEAK 2(15Q22.31) WILD-TYPE 18 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) MUTATED      7   14
  AMP PEAK 2(15Q22.31) WILD-TYPE   18   25
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  FEMALE                            7                             18
  MALE                             14                             25
D2V8, continuous
D2V9, continuous
D2V10, continuous
> q(save="no")
