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ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvs_onlysig.49.4134/CNV2ClinicalAnalysis_nozzle_onlysig_focal.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvs_onlysig.49.4134/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/416912/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/3351134/KICH-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KICH-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KICH-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=25, in cluster file=66, common to both=25
[1]  2 25
[1] "Amp Peak 1(8q11.23)"
[1] 3
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                           10                            15 
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                           10                            15 
[1] "Amp Peak 2(15q22.31)"
[1] 3
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                            10                             15 
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                            10                             15 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[11] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[13] "YEAROFTOBACCOSMOKINGONSET"        "DISTANT.METASTASIS"              
[15] "LYMPH.NODE.METASTASIS"            "TUMOR.STAGECODE"                 
[17] "NEOPLASM.DISEASESTAGE"            "BATCHNUMBER"                     

Input Data has 18 rows and 25 columns.

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

Clustering(1) Variable = Amp Peak 1(8q11.23)
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 1(8Q11.23) CNV        7  2
  AMP PEAK 1(8Q11.23) WILD-TYPE 15  0
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                            9                            15 
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                            2                             0 
$`AMP PEAK 1(8Q11.23) CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       28.08       142.52        23.47        25.91         3.52         0.56 
TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8409 
       52.27        11.21        80.38 

$`AMP PEAK 1(8Q11.23) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77         8.12        51.02       114.18        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19        72.69        67.82        23.41         2.50        36.95 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       89.65        20.91        75.72 

      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                         0.56                          2.50 
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                       142.52                        114.18 
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                        25.91                         65.19 
[1] "0.6 - 142.5 (25.9)" "2.5 - 114.2 (65.2)"
                   TCGA-KL-8328                    TCGA-KL-8339 
"AMP PEAK 1(8Q11.23) WILD-TYPE"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KM-8438                    TCGA-KM-8439 
      "AMP PEAK 1(8Q11.23) CNV" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8477                    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) CNV" "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) CNV" 
                   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) CNV"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KN-8428                    TCGA-KN-8429 
      "AMP PEAK 1(8Q11.23) CNV" "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) CNV" "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-8409 
"AMP PEAK 1(8Q11.23) WILD-TYPE"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KL-8328                    TCGA-KL-8339 
"AMP PEAK 1(8Q11.23) WILD-TYPE"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KM-8438                    TCGA-KM-8439 
      "AMP PEAK 1(8Q11.23) CNV" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8477                    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) CNV" "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) CNV" 
                   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) CNV"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KN-8428                    TCGA-KN-8429 
      "AMP PEAK 1(8Q11.23) CNV" "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) CNV" "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-8409 
"AMP PEAK 1(8Q11.23) WILD-TYPE"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KL-8328                    TCGA-KL-8339 
"AMP PEAK 1(8Q11.23) WILD-TYPE"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KM-8438                    TCGA-KM-8439 
      "AMP PEAK 1(8Q11.23) CNV" "AMP PEAK 1(8Q11.23) WILD-TYPE" 
                   TCGA-KM-8477                    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) CNV" "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) CNV" 
                   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) CNV"       "AMP PEAK 1(8Q11.23) CNV" 
                   TCGA-KN-8428                    TCGA-KN-8429 
      "AMP PEAK 1(8Q11.23) CNV" "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) CNV" "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-8409 
"AMP PEAK 1(8Q11.23) WILD-TYPE"       "AMP PEAK 1(8Q11.23) CNV" 
[1] "hr="     "7.2e+09"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(8Q11.23) CNV          2    8
  AMP PEAK 1(8Q11.23) WILD-TYPE    9    6
        clus
vv       AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  FEMALE                       2                             9
  MALE                         8                             6
                               vv
clus                            M0 M1 MX
  AMP PEAK 1(8Q11.23) CNV        1  2  1
  AMP PEAK 1(8Q11.23) WILD-TYPE  1  0  2
D1V4, multiclass
    clus
vv   AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  M0                       1                             1
  M1                       2                             0
  MX                       1                             2
                               vv
clus                            N0 N1 NX
  AMP PEAK 1(8Q11.23) CNV        6  2  2
  AMP PEAK 1(8Q11.23) WILD-TYPE  7  0  8
D1V5, multiclass
    clus
vv   AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  N0                       6                             7
  N1                       2                             0
  NX                       2                             8
D1V6, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(8Q11.23) CNV             2        4         1        3
  AMP PEAK 1(8Q11.23) WILD-TYPE       6        8         1        0
D1V7, multiclass
           clus
vv          AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  STAGE I                         2                             6
  STAGE II                        4                             8
  STAGE III                       1                             1
  STAGE IV                        3                             0

Clustering(2) Variable = Amp Peak 2(15q22.31)
D2V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 2(15Q22.31) CNV        7  2
  AMP PEAK 2(15Q22.31) WILD-TYPE 15  0
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                             9                             15 
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                             2                              0 
$`AMP PEAK 2(15Q22.31) CNV`
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       28.08       142.52        23.47        72.69         3.52        52.27 
TCGA-KN-8433 TCGA-KN-8435 TCGA-KO-8409 
       11.21        89.65        80.38 

$`AMP PEAK 2(15Q22.31) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77         8.12        51.02       114.18        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.91        65.19         0.56        67.82        23.41         2.50 
TCGA-KN-8434 TCGA-KN-8436 TCGA-KN-8437 
       36.95        20.91        75.72 

      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                          3.52                           0.56 
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                        142.52                         114.18 
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                         52.27                          36.95 
[1] "3.5 - 142.5 (52.3)" "0.6 - 114.2 (37.0)"
                    TCGA-KL-8328                     TCGA-KL-8339 
"AMP PEAK 2(15Q22.31) WILD-TYPE"       "AMP PEAK 2(15Q22.31) CNV" 
                    TCGA-KM-8438                     TCGA-KM-8439 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8477                     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) CNV" "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) CNV" 
                    TCGA-KN-8426                     TCGA-KN-8427 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8428                     TCGA-KN-8429 
      "AMP PEAK 2(15Q22.31) CNV" "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) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8435                     TCGA-KN-8436 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8437                     TCGA-KO-8409 
"AMP PEAK 2(15Q22.31) WILD-TYPE"       "AMP PEAK 2(15Q22.31) CNV" 
                    TCGA-KL-8328                     TCGA-KL-8339 
"AMP PEAK 2(15Q22.31) WILD-TYPE"       "AMP PEAK 2(15Q22.31) CNV" 
                    TCGA-KM-8438                     TCGA-KM-8439 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8477                     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) CNV" "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) CNV" 
                    TCGA-KN-8426                     TCGA-KN-8427 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8428                     TCGA-KN-8429 
      "AMP PEAK 2(15Q22.31) CNV" "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) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8435                     TCGA-KN-8436 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8437                     TCGA-KO-8409 
"AMP PEAK 2(15Q22.31) WILD-TYPE"       "AMP PEAK 2(15Q22.31) CNV" 
                    TCGA-KL-8328                     TCGA-KL-8339 
"AMP PEAK 2(15Q22.31) WILD-TYPE"       "AMP PEAK 2(15Q22.31) CNV" 
                    TCGA-KM-8438                     TCGA-KM-8439 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KM-8477                     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) CNV" "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) CNV" 
                    TCGA-KN-8426                     TCGA-KN-8427 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8428                     TCGA-KN-8429 
      "AMP PEAK 2(15Q22.31) CNV" "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) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8435                     TCGA-KN-8436 
      "AMP PEAK 2(15Q22.31) CNV" "AMP PEAK 2(15Q22.31) WILD-TYPE" 
                    TCGA-KN-8437                     TCGA-KO-8409 
"AMP PEAK 2(15Q22.31) WILD-TYPE"       "AMP PEAK 2(15Q22.31) CNV" 
[1] "hr="     "2.1e+09"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) CNV          2    8
  AMP PEAK 2(15Q22.31) WILD-TYPE    9    6
        clus
vv       AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  FEMALE                        2                              9
  MALE                          8                              6
                                vv
clus                             M0 M1 MX
  AMP PEAK 2(15Q22.31) CNV        1  2  1
  AMP PEAK 2(15Q22.31) WILD-TYPE  1  0  2
D2V4, multiclass
    clus
vv   AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  M0                        1                              1
  M1                        2                              0
  MX                        1                              2
                                vv
clus                             N0 N1 NX
  AMP PEAK 2(15Q22.31) CNV        6  1  3
  AMP PEAK 2(15Q22.31) WILD-TYPE  7  1  7
D2V5, multiclass
    clus
vv   AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  N0                        6                              7
  N1                        1                              1
  NX                        3                              7
D2V6, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(15Q22.31) CNV             2        5         1        2
  AMP PEAK 2(15Q22.31) WILD-TYPE       6        7         1        1
D2V7, multiclass
           clus
vv          AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  STAGE I                          2                              6
  STAGE II                         5                              7
  STAGE III                        1                              1
  STAGE IV                         2                              1
                   V1.D                      V2                      V3 
        "Time to Death"                   "AGE"                "GENDER" 
                     V4                      V5                      V6 
   "DISTANT.METASTASIS" "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE" 
                     V7 
"NEOPLASM.DISEASESTAGE" 
> q(save="no")
