
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_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/ESCA-TP/4428761/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/ESCA-TP/4428472/ESCA-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=ESCA-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=ESCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=63, in cluster file=63, common to both=63
[1] "Reduce the number of clustering variables from 80 to 71."
[1] 71 63
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                7                56 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                7                56 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               17                46 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               17                46 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               11                52 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               11                52 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                7                56 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                7                56 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                9                54 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                9                54 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               19                44 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               19                44 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4                59 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4                59 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               20                43 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               20                43 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                5                58 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                5                58 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                60 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                60 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               28                35 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               28                35 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               19                44 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               19                44 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               17                46 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               17                46 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               26                37 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               26                37 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                3                60 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                3                60 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8                55 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8                55 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 6                 57 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 6                 57 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                 60 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                 60 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 3                 60 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 3                 60 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 3                 60 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 3                 60 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                21                 42 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                21                 42 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 9                 54 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 9                 54 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 8                 55 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 8                 55 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 9                 54 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 9                 54 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 4                 59 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 4                 59 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 5                 58 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 5                 58 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 4                 59 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 4                 59 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 7                 56 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 7                 56 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 7                 56 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 7                 56 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                14                 49 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                14                 49 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 3                 60 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 3                 60 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 3                 60 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 3                 60 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 7                 56 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 7                 56 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                25                 38 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                25                 38 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                27                 36 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                27                 36 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                 60 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                 60 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 8                 55 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 8                 55 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               10                53 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               10                53 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               26                37 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               26                37 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                4                59 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                4                59 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               23                40 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               23                40 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               18                45 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               18                45 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
                9                54 
      5P LOSS CNV 5P LOSS WILD-TYPE 
                9                54 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               17                46 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               17                46 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               10                53 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               10                53 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                7                56 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                7                56 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
                3                60 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                3                60 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               14                49 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               14                49 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6                57 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6                57 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               23                40 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               23                40 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               10                53 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               10                53 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                13                 50 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                13                 50 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                15                 48 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                15                 48 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                11                 52 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                11                 52 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                16                 47 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                16                 47 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 8                 55 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 8                 55 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 6                 57 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 6                 57 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                15                 48 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                15                 48 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 7                 56 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 7                 56 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 9                 54 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 9                 54 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                10                 53 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                10                 53 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                11                 52 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                11                 52 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                14                 49 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                14                 49 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                12                 51 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                12                 51 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                24                 39 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                24                 39 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 9                 54 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 9                 54 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 6                 57 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 6                 57 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                 58 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                 58 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                27                 36 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                27                 36 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                11                 52 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                11                 52 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3                60 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3                60 
[1] "data2feature, selection="
[1] "CN_CNMF"          "METHLYATION_CNMF"

Input Data has 2 rows and 63 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"          "METHLYATION_CNMF"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 63 columns, 0 survival variables, and 2 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4                18
  CLUS_2           1                14
  CLUS_3           2                24
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4                26
  CLUS_2           2                12
  CLUS_3           1                18

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           7                15
  CLUS_2           5                10
  CLUS_3           5                21
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           9                21
  CLUS_2           4                10
  CLUS_3           4                15

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           7                15
  CLUS_2           2                13
  CLUS_3           2                24
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           8                22
  CLUS_2           1                13
  CLUS_3           2                17

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                17
  CLUS_2           2                13
  CLUS_3           0                26
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           6                24
  CLUS_2           0                14
  CLUS_3           1                18

Clustering(5) Variable = 3p gain
D5V1, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           7                15
  CLUS_2           1                14
  CLUS_3           1                25
D5V2, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           7                23
  CLUS_2           1                13
  CLUS_3           1                18

Clustering(6) Variable = 3q gain
D6V1, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          11                11
  CLUS_2           7                 8
  CLUS_3           1                25
D6V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          17                13
  CLUS_2           1                13
  CLUS_3           1                18

Clustering(7) Variable = 4p gain
D7V1, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3                19
  CLUS_2           0                15
  CLUS_3           1                25
D7V2, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                28
  CLUS_2           1                13
  CLUS_3           1                18

Clustering(8) Variable = 5p gain
D8V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           9                13
  CLUS_2           4                11
  CLUS_3           7                19
D8V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          11                19
  CLUS_2           3                11
  CLUS_3           6                13

Clustering(9) Variable = 6p gain
D9V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                20
  CLUS_2           2                13
  CLUS_3           1                25
D9V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3                27
  CLUS_2           1                13
  CLUS_3           1                18

Clustering(10) Variable = 6q gain
D10V1, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                22
  CLUS_2           3                12
  CLUS_3           0                26
D10V2, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2                28
  CLUS_2           0                14
  CLUS_3           1                18

Clustering(11) Variable = 7p gain
D11V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          11                11
  CLUS_2           9                 6
  CLUS_3           8                18
D11V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          15                15
  CLUS_2           4                10
  CLUS_3           9                10

Clustering(12) Variable = 7q gain
D12V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           8                14
  CLUS_2           5                10
  CLUS_3           6                20
D12V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          11                19
  CLUS_2           2                12
  CLUS_3           6                13

Clustering(13) Variable = 8p gain
D13V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           4                18
  CLUS_2           6                 9
  CLUS_3           7                19
D13V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           9                21
  CLUS_2           1                13
  CLUS_3           7                12

Clustering(14) Variable = 8q gain
D14V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           9                13
  CLUS_2           7                 8
  CLUS_3          10                16
D14V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          14                16
  CLUS_2           4                10
  CLUS_3           8                11

Clustering(15) Variable = 9p gain
D15V1, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                21
  CLUS_2           2                13
  CLUS_3           0                26
D15V2, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                27
  CLUS_2           0                14
  CLUS_3           0                19

Clustering(16) Variable = 9q gain
D16V1, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                20
  CLUS_2           4                11
  CLUS_3           2                24
D16V2, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           6                24
  CLUS_2           1                13
  CLUS_3           1                18

Clustering(17) Variable = 10p gain
D17V1, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            1                 14
  CLUS_3            3                 23
D17V2, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            0                 14
  CLUS_3            3                 16

Clustering(18) Variable = 10q gain
D18V1, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 22
  CLUS_2            2                 13
  CLUS_3            1                 25
D18V2, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            0                 14
  CLUS_3            1                 18

Clustering(19) Variable = 11p gain
D19V1, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 22
  CLUS_2            3                 12
  CLUS_3            0                 26
D19V2, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 13
  CLUS_3            0                 19

Clustering(20) Variable = 11q gain
D20V1, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 22
  CLUS_2            3                 12
  CLUS_3            0                 26
D20V2, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            1                 13
  CLUS_3            1                 18

Clustering(21) Variable = 12p gain
D21V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           12                 10
  CLUS_2            7                  8
  CLUS_3            2                 24
D21V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           16                 14
  CLUS_2            3                 11
  CLUS_3            2                 17

Clustering(22) Variable = 12q gain
D22V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            4                 18
  CLUS_2            4                 11
  CLUS_3            1                 25
D22V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            7                 23
  CLUS_2            1                 13
  CLUS_3            1                 18

Clustering(23) Variable = 13q gain
D23V1, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 21
  CLUS_2            2                 13
  CLUS_3            5                 21
D23V2, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            1                 13
  CLUS_3            6                 13

Clustering(24) Variable = 14q gain
D24V1, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            3                 19
  CLUS_2            3                 12
  CLUS_3            3                 23
D24V2, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            7                 23
  CLUS_2            0                 14
  CLUS_3            2                 17

Clustering(25) Variable = 15q gain
D25V1, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            0                 15
  CLUS_3            2                 24
D25V2, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            0                 14
  CLUS_3            2                 17

Clustering(26) Variable = 16p gain
D26V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            1                 14
  CLUS_3            2                 24
D26V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            1                 13
  CLUS_3            0                 19

Clustering(27) Variable = 16q gain
D27V1, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            0                 15
  CLUS_3            2                 24
D27V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            1                 13
  CLUS_3            0                 19

Clustering(28) Variable = 17p gain
D28V1, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            5                 10
  CLUS_3            0                 26
D28V2, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            6                 24
  CLUS_2            1                 13
  CLUS_3            0                 19

Clustering(29) Variable = 17q gain
D29V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            4                 11
  CLUS_3            1                 25
D29V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            5                 25
  CLUS_2            1                 13
  CLUS_3            1                 18

Clustering(30) Variable = 18p gain
D30V1, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            5                 17
  CLUS_2            7                  8
  CLUS_3            2                 24
D30V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           10                 20
  CLUS_2            3                 11
  CLUS_3            1                 18

Clustering(31) Variable = 18q gain
D31V1, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            0                 15
  CLUS_3            1                 25
D31V2, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            1                 13
  CLUS_3            1                 18

Clustering(32) Variable = 19p gain
D32V1, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 22
  CLUS_2            3                 12
  CLUS_3            0                 26
D32V2, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 13
  CLUS_3            0                 19

Clustering(33) Variable = 19q gain
D33V1, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                 22
  CLUS_2            5                 10
  CLUS_3            2                 24
D33V2, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 13
  CLUS_3            4                 15

Clustering(34) Variable = 20p gain
D34V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           10                 12
  CLUS_2            6                  9
  CLUS_3            9                 17
D34V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           12                 18
  CLUS_2            7                  7
  CLUS_3            6                 13

Clustering(35) Variable = 20q gain
D35V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            8                 14
  CLUS_2            7                  8
  CLUS_3           12                 14
D35V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           10                 20
  CLUS_2            7                  7
  CLUS_3           10                  9

Clustering(36) Variable = 21q gain
D36V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 21
  CLUS_2            2                 13
  CLUS_3            0                 26
D36V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            0                 14
  CLUS_3            0                 19

Clustering(37) Variable = 22q gain
D37V1, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 19
  CLUS_2            2                 13
  CLUS_3            3                 23
D37V2, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            6                 24
  CLUS_2            1                 13
  CLUS_3            1                 18

Clustering(38) Variable = Xq gain
D38V1, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           6                16
  CLUS_2           2                13
  CLUS_3           2                24
D38V2, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           8                22
  CLUS_2           2                12
  CLUS_3           0                19

Clustering(39) Variable = 3p loss
D39V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           8                14
  CLUS_2           8                 7
  CLUS_3          10                16
D39V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          14                16
  CLUS_2           5                 9
  CLUS_3           7                12

Clustering(40) Variable = 3q loss
D40V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                21
  CLUS_2           2                13
  CLUS_3           1                25
D40V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2           0                14
  CLUS_3           2                17

Clustering(41) Variable = 4p loss
D41V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          11                11
  CLUS_2           7                 8
  CLUS_3           5                21
D41V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          15                15
  CLUS_2           1                13
  CLUS_3           7                12

Clustering(42) Variable = 4q loss
D42V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           8                14
  CLUS_2           6                 9
  CLUS_3           4                22
D42V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          12                18
  CLUS_2           0                14
  CLUS_3           6                13

Clustering(43) Variable = 5p loss
D43V1, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                20
  CLUS_2           4                11
  CLUS_3           3                23
D43V2, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           5                25
  CLUS_2           0                14
  CLUS_3           4                15

Clustering(44) Variable = 5q loss
D44V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6                16
  CLUS_2           5                10
  CLUS_3           6                20
D44V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          10                20
  CLUS_2           0                14
  CLUS_3           7                12

Clustering(45) Variable = 6p loss
D45V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           5                17
  CLUS_2           3                12
  CLUS_3           2                24
D45V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           8                22
  CLUS_2           1                13
  CLUS_3           1                18

Clustering(46) Variable = 6q loss
D46V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           4                18
  CLUS_2           2                13
  CLUS_3           1                25
D46V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           6                24
  CLUS_2           1                13
  CLUS_3           0                19

Clustering(47) Variable = 7p loss
D47V1, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                21
  CLUS_2           2                13
  CLUS_3           0                26
D47V2, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           3                27
  CLUS_2           0                14
  CLUS_3           0                19

Clustering(48) Variable = 8p loss
D48V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           6                16
  CLUS_2           3                12
  CLUS_3           5                21
D48V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           8                22
  CLUS_2           2                12
  CLUS_3           4                15

Clustering(49) Variable = 8q loss
D49V1, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           2                20
  CLUS_2           1                14
  CLUS_3           3                23
D49V2, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2           1                13
  CLUS_3           3                16

Clustering(50) Variable = 9p loss
D50V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          10                12
  CLUS_2           6                 9
  CLUS_3           7                19
D50V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          13                17
  CLUS_2           2                12
  CLUS_3           8                11

Clustering(51) Variable = 9q loss
D51V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           6                16
  CLUS_2           2                13
  CLUS_3           2                24
D51V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           7                23
  CLUS_2           0                14
  CLUS_3           3                16

Clustering(52) Variable = 10p loss
D52V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            7                 15
  CLUS_2            3                 12
  CLUS_3            3                 23
D52V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            9                 21
  CLUS_2            2                 12
  CLUS_3            2                 17

Clustering(53) Variable = 10q loss
D53V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           11                 11
  CLUS_2            2                 13
  CLUS_3            2                 24
D53V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           12                 18
  CLUS_2            1                 13
  CLUS_3            2                 17

Clustering(54) Variable = 11p loss
D54V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                 15
  CLUS_2            1                 14
  CLUS_3            3                 23
D54V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            8                 22
  CLUS_2            0                 14
  CLUS_3            3                 16

Clustering(55) Variable = 11q loss
D55V1, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           12                 10
  CLUS_2            2                 13
  CLUS_3            2                 24
D55V2, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           13                 17
  CLUS_2            1                 13
  CLUS_3            2                 17

Clustering(56) Variable = 12p loss
D56V1, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            3                 12
  CLUS_3            3                 23
D56V2, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            2                 12
  CLUS_3            4                 15

Clustering(57) Variable = 12q loss
D57V1, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 21
  CLUS_2            2                 13
  CLUS_3            3                 23
D57V2, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            1                 13
  CLUS_3            4                 15

Clustering(58) Variable = 13q loss
D58V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            9                 13
  CLUS_2            4                 11
  CLUS_3            2                 24
D58V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           12                 18
  CLUS_2            2                 12
  CLUS_3            1                 18

Clustering(59) Variable = 14q loss
D59V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            2                 13
  CLUS_3            3                 23
D59V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            2                 12
  CLUS_3            3                 16

Clustering(60) Variable = 15q loss
D60V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                 18
  CLUS_2            3                 12
  CLUS_3            2                 24
D60V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            2                 12
  CLUS_3            3                 16

Clustering(61) Variable = 16p loss
D61V1, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            1                 21
  CLUS_2            2                 13
  CLUS_3            7                 19
D61V2, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            2                 12
  CLUS_3            6                 13

Clustering(62) Variable = 16q loss
D62V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 21
  CLUS_2            4                 11
  CLUS_3            6                 20
D62V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            2                 12
  CLUS_3            5                 14

Clustering(63) Variable = 17p loss
D63V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                 19
  CLUS_2            2                 13
  CLUS_3            9                 17
D63V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            2                 12
  CLUS_3           10                  9

Clustering(64) Variable = 18p loss
D64V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 18
  CLUS_2            1                 14
  CLUS_3            7                 19
D64V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            2                 12
  CLUS_3            6                 13

Clustering(65) Variable = 18q loss
D65V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           10                 12
  CLUS_2            4                 11
  CLUS_3           10                 16
D65V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           12                 18
  CLUS_2            2                 12
  CLUS_3           10                  9

Clustering(66) Variable = 19p loss
D66V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            6                 16
  CLUS_2            1                 14
  CLUS_3            2                 24
D66V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            5                 25
  CLUS_2            2                 12
  CLUS_3            2                 17

Clustering(67) Variable = 19q loss
D67V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            4                 18
  CLUS_2            0                 15
  CLUS_3            2                 24
D67V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            2                 12
  CLUS_3            1                 18

Clustering(68) Variable = 20p loss
D68V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 21
  CLUS_2            3                 12
  CLUS_3            1                 25
D68V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            1                 13
  CLUS_3            1                 18

Clustering(69) Variable = 21q loss
D69V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           10                 12
  CLUS_2            5                 10
  CLUS_3           12                 14
D69V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           12                 18
  CLUS_2            5                  9
  CLUS_3           10                  9

Clustering(70) Variable = 22q loss
D70V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                 20
  CLUS_2            2                 13
  CLUS_3            7                 19
D70V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            2                 12
  CLUS_3            7                 12

Clustering(71) Variable = Xq loss
D71V1, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                21
  CLUS_2           0                15
  CLUS_3           2                24
D71V2, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                29
  CLUS_2           0                14
  CLUS_3           2                17
                V1                 V2 
         "CN_CNMF" "METHLYATION_CNMF" 
> q(save="no")
