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

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

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

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

> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/335533/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SARC-TP/2667025/1.GDAC_mergedClustering.Finished/SARC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SARC-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=SARC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=52, in cluster file=29, common to both=29
[1] "Reduce the number of clustering variables from 80 to 46."
[1] 46 29
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                25 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                25 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                25 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                25 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                25 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                25 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                24 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                24 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                24 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                24 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                24 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                24 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                24 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                24 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                25 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                25 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                26 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                26 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                24 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                24 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 26 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 26 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 26 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 26 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 26 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 26 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 4                 25 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 4                 25 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 24 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 24 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                24 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                24 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                26 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                26 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                26 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                26 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                26 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                26 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                25 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                25 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                24 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                24 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                26 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                26 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                23 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                23 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                26 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                26 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                25 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                25 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                24 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                24 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                5                24 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                5                24 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                26 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                26 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 21 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 21 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 19 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 19 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 22 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 22 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 23 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 23 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                12                 17 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                12                 17 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 8                 21 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 8                 21 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 23 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 24 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 24 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 9                 20 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 9                 20 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 24 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 24 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 26 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 26 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 25 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 25 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 25 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 25 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 26 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 26 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 23 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 23 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 23 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                11                 18 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                11                 18 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                23 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"              "METHLYATION_CNMF"     "MIRSEQ_CNMF"         
[4] "MIRSEQ_CHIERARCHICAL"

Input Data has 4 rows and 29 columns.

Variable 1:'CN_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"              "METHLYATION_CNMF"     "MIRSEQ_CNMF"         
[4] "MIRSEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 29 columns, 0 survival variables, and 4 non-survival variables.
CN_CNMF, nv=2, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 5p gain mutation analysis
D1V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    0
  5P GAIN WILD-TYPE   14   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               0                11
D1V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               1                 9
  CLUS_3               1                 7
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    2
  5P GAIN WILD-TYPE   14   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                11
D1V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(2) Variable = 5q gain mutation analysis
D2V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    0
  5Q GAIN WILD-TYPE   14   11
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               0                11
D2V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                 8
  CLUS_3               0                 8
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    2
  5Q GAIN WILD-TYPE   14   11
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                11
D2V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(3) Variable = 6p gain mutation analysis
D3V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    2
  6P GAIN WILD-TYPE   16    9
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                 9
D3V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                 8
  CLUS_3               0                 8
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    0
  6P GAIN WILD-TYPE   12   13
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               0                13
D3V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               4                12

Clustering(4) Variable = 6q gain mutation analysis
D4V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    4
  6Q GAIN WILD-TYPE   17    7
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               4                 7
D4V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               2                 8
  CLUS_3               0                 8
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5    0
  6Q GAIN WILD-TYPE   11   13
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                11
  CLUS_2               0                13
D4V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               5                11

Clustering(5) Variable = 7p gain mutation analysis
D5V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    1
  7P GAIN WILD-TYPE   14   10
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                10
D5V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               2                 8
  CLUS_3               0                 8
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2    3
  7P GAIN WILD-TYPE   14   10
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                10
D5V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(6) Variable = 7q gain mutation analysis
D6V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    1
  7Q GAIN WILD-TYPE   14   10
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                10
D6V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               2                 8
  CLUS_3               0                 8
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    3
  7Q GAIN WILD-TYPE   14   10
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                10
D6V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(7) Variable = 8p gain mutation analysis
D7V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    0
  8P GAIN WILD-TYPE   13   11
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2               0                11
D7V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               2                 8
  CLUS_3               2                 6
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    3
  8P GAIN WILD-TYPE   14   10
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                10
D7V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               3                 9
  CLUS_3               2                14

Clustering(8) Variable = 8q gain mutation analysis
D8V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3    1
  8Q GAIN WILD-TYPE   15   10
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                10
D8V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               2                 8
  CLUS_3               2                 6
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    2
  8Q GAIN WILD-TYPE   14   11
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                11
D8V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(9) Variable = 9p gain mutation analysis
D9V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE   16   10
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                10
D9V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               1                 7
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE   14   12
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D9V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(10) Variable = 9q gain mutation analysis
D10V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    3
  9Q GAIN WILD-TYPE   16    8
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                 8
D10V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               3                 7
  CLUS_3               1                 7
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    1
  9Q GAIN WILD-TYPE   12   12
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               1                12
D10V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               4                12

Clustering(11) Variable = 16p gain mutation analysis
D11V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    1
  16P GAIN WILD-TYPE   16   10
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 10
D11V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                  8
  CLUS_3                1                  7
D11V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    2
  16P GAIN WILD-TYPE   15   11
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D11V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                1                 15

Clustering(12) Variable = 17q gain mutation analysis
D12V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    0
  17Q GAIN WILD-TYPE   15   11
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                0                 11
D12V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                  8
  CLUS_3                1                  7
D12V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    2
  17Q GAIN WILD-TYPE   15   11
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D12V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                1                 11
  CLUS_3                1                 15

Clustering(13) Variable = 18q gain mutation analysis
D13V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    1
  18Q GAIN WILD-TYPE   16   10
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 10
D13V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                3                  7
  CLUS_3                0                  8
D13V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    1
  18Q GAIN WILD-TYPE   14   12
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 12
D13V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                2                 14

Clustering(14) Variable = 20p gain mutation analysis
D14V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4    0
  20P GAIN WILD-TYPE   14   11
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                0                 11
D14V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                3                  7
  CLUS_3                1                  7
D14V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    2
  20P GAIN WILD-TYPE   14   11
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                 11
D14V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                2                 14

Clustering(15) Variable = 20q gain mutation analysis
D15V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    1
  20Q GAIN WILD-TYPE   14   10
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                1                 10
D15V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                4                  6
  CLUS_3                1                  7
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3    2
  20Q GAIN WILD-TYPE   13   11
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                2                 11
D15V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                3                 13

Clustering(16) Variable = 1p loss mutation analysis
D16V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    0
  1P LOSS WILD-TYPE   13   11
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               0                11
D16V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               3                 5
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    4
  1P LOSS WILD-TYPE   15    9
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               4                 9
D16V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               3                 9
  CLUS_3               1                15

Clustering(17) Variable = 1q loss mutation analysis
D17V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE   15   11
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                11
D17V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               1                 7
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    1
  1Q LOSS WILD-TYPE   14   12
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D17V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(18) Variable = 2p loss mutation analysis
D18V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    0
  2P LOSS WILD-TYPE   15   11
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                11
D18V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               1                 9
  CLUS_3               2                 6
D18V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    2
  2P LOSS WILD-TYPE   15   11
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                11
D18V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               1                15

Clustering(19) Variable = 2q loss mutation analysis
D19V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    1
  2Q LOSS WILD-TYPE   16   10
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                10
D19V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               2                 8
  CLUS_3               1                 7
D19V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    1
  2Q LOSS WILD-TYPE   14   12
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D19V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(20) Variable = 3p loss mutation analysis
D20V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    4
  3P LOSS WILD-TYPE   18    7
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               4                 7
D20V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                 8
  CLUS_3               0                 8
D20V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    0
  3P LOSS WILD-TYPE   12   13
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                12
  CLUS_2               0                13
D20V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               4                12

Clustering(21) Variable = 3q loss mutation analysis
D21V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    4
  3Q LOSS WILD-TYPE   17    7
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               4                 7
D21V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                 8
  CLUS_3               1                 7
D21V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    1
  3Q LOSS WILD-TYPE   12   12
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4                12
  CLUS_2               1                12
D21V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               4                12

Clustering(22) Variable = 5p loss mutation analysis
D22V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    1
  5P LOSS WILD-TYPE   16   10
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                10
D22V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               0                10
  CLUS_3               1                 7
D22V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    1
  5P LOSS WILD-TYPE   14   12
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D22V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(23) Variable = 6p loss mutation analysis
D23V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    2
  6P LOSS WILD-TYPE   14    9
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                 9
D23V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               1                 9
  CLUS_3               3                 5
D23V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    4
  6P LOSS WILD-TYPE   14    9
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               4                 9
D23V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               4                 8
  CLUS_3               2                14

Clustering(24) Variable = 7p loss mutation analysis
D24V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE   15   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                11
D24V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               1                 9
  CLUS_3               2                 6
D24V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    2
  7P LOSS WILD-TYPE   15   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                11
D24V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               1                15

Clustering(25) Variable = 7q loss mutation analysis
D25V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE   15   10
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                10
D25V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               3                 7
  CLUS_3               1                 7
D25V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE   13   12
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               1                12
D25V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               3                13

Clustering(26) Variable = 8p loss mutation analysis
D26V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    2
  8P LOSS WILD-TYPE   15    9
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                 9
D26V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                 8
  CLUS_3               1                 7
D26V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    2
  8P LOSS WILD-TYPE   13   11
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               2                11
D26V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               1                11
  CLUS_3               3                13

Clustering(27) Variable = 9p loss mutation analysis
D27V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3    2
  9P LOSS WILD-TYPE   15    9
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                 9
D27V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               4                 6
  CLUS_3               0                 8
D27V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4    1
  9P LOSS WILD-TYPE   12   12
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                12
  CLUS_2               1                12
D27V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               0                12
  CLUS_3               4                12

Clustering(28) Variable = 9q loss mutation analysis
D28V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    0
  9Q LOSS WILD-TYPE   15   11
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                11
D28V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               1                 7
D28V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2    1
  9Q LOSS WILD-TYPE   14   12
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D28V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(29) Variable = 10p loss mutation analysis
D29V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7    1
  10P LOSS WILD-TYPE   11   10
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                1                 10
D29V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                4                  6
  CLUS_3                2                  6
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    4
  10P LOSS WILD-TYPE   12    9
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                4                  9
D29V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                3                  9
  CLUS_3                4                 12

Clustering(30) Variable = 10q loss mutation analysis
D30V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9    1
  10Q LOSS WILD-TYPE    9   10
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                9                  9
  CLUS_2                1                 10
D30V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                4                  6
  CLUS_3                4                  4
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    7
  10Q LOSS WILD-TYPE   13    6
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                7                  6
D30V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                6                  6
  CLUS_3                3                 13

Clustering(31) Variable = 11p loss mutation analysis
D31V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    3
  11P LOSS WILD-TYPE   14    8
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                  8
D31V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                5                  5
  CLUS_3                1                  7
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    2
  11P LOSS WILD-TYPE   11   11
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                2                 11
D31V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                1                 11
  CLUS_3                5                 11

Clustering(32) Variable = 11q loss mutation analysis
D32V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    3
  11Q LOSS WILD-TYPE   15    8
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                  8
D32V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                4                  6
  CLUS_3                1                  7
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5    1
  11Q LOSS WILD-TYPE   11   12
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                1                 12
D32V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                5                 11

Clustering(33) Variable = 13q loss mutation analysis
D33V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    3
  13Q LOSS WILD-TYPE    9    8
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                  9
  CLUS_2                3                  8
D33V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                5                  5
  CLUS_3                5                  3
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    6
  13Q LOSS WILD-TYPE   10    7
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                6                  7
D33V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                5                  7
  CLUS_3                6                 10

Clustering(34) Variable = 14q loss mutation analysis
D34V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5    3
  14Q LOSS WILD-TYPE   13    8
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                3                  8
D34V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                2                  8
  CLUS_3                4                  4
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    5
  14Q LOSS WILD-TYPE   13    8
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                5                  8
D34V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                5                  7
  CLUS_3                3                 13

Clustering(35) Variable = 15q loss mutation analysis
D35V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    4
  15Q LOSS WILD-TYPE   16    7
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                4                  7
D35V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                  7
  CLUS_2                2                  8
  CLUS_3                0                  8
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    0
  15Q LOSS WILD-TYPE   10   13
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                0                 13
D35V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                0                 12
  CLUS_3                6                 10

Clustering(36) Variable = 16p loss mutation analysis
D36V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    2
  16P LOSS WILD-TYPE   15    9
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                  9
D36V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                2                  8
  CLUS_3                1                  7
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    1
  16P LOSS WILD-TYPE   12   12
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                1                 12
D36V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                4                 12

Clustering(37) Variable = 16q loss mutation analysis
D37V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6    3
  16Q LOSS WILD-TYPE   12    8
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                3                  8
D37V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                4                  6
  CLUS_3                3                  5
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    5
  16Q LOSS WILD-TYPE   12    8
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                5                  8
D37V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                4                  8
  CLUS_3                4                 12

Clustering(38) Variable = 17p loss mutation analysis
D38V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    1
  17P LOSS WILD-TYPE   14   10
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                1                 10
D38V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                0                 10
  CLUS_3                3                  5
D38V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    3
  17P LOSS WILD-TYPE   14   10
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                3                 10
D38V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                3                  9
  CLUS_3                2                 14

Clustering(39) Variable = 17q loss mutation analysis
D39V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    1
  17Q LOSS WILD-TYPE   16   10
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 10
D39V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                0                 10
  CLUS_3                2                  6
D39V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE   15   11
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D39V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                1                 15

Clustering(40) Variable = 18p loss mutation analysis
D40V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    1
  18P LOSS WILD-TYPE   15   10
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 10
D40V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                1                  9
  CLUS_3                1                  7
D40V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    1
  18P LOSS WILD-TYPE   13   12
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                 12
D40V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                3                 13

Clustering(41) Variable = 18q loss mutation analysis
D41V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE   15   10
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 10
D41V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                1                  9
  CLUS_3                1                  7
D41V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE   13   12
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                 12
D41V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                3                 13

Clustering(42) Variable = 19q loss mutation analysis
D42V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    0
  19Q LOSS WILD-TYPE   15   11
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                0                 11
D42V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                  8
  CLUS_3                1                  7
D42V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   15   11
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D42V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                1                 11
  CLUS_3                1                 15

Clustering(43) Variable = 20p loss mutation analysis
D43V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    5
  20P LOSS WILD-TYPE   17    6
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                5                  6
D43V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                2                  8
  CLUS_3                1                  7
D43V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    1
  20P LOSS WILD-TYPE   11   12
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                1                 12
D43V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                5                 11

Clustering(44) Variable = 21q loss mutation analysis
D44V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    3
  21Q LOSS WILD-TYPE   15    8
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                  8
D44V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                3                  7
  CLUS_3                1                  7
D44V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    2
  21Q LOSS WILD-TYPE   12   11
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                2                 11
D44V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                4                 12

Clustering(45) Variable = 22q loss mutation analysis
D45V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    4
  22Q LOSS WILD-TYPE   11    7
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                4                  7
D45V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                4                  6
  CLUS_3                4                  4
D45V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    4
  22Q LOSS WILD-TYPE    9    9
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                7                  9
  CLUS_2                4                  9
D45V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                4                  8
  CLUS_3                7                  9

Clustering(46) Variable = Xq loss mutation analysis
D46V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    2
  XQ LOSS WILD-TYPE   14    9
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                 9
D46V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               3                 7
  CLUS_3               3                 5
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    3
  XQ LOSS WILD-TYPE   13   10
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               3                10
D46V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               3                 9
  CLUS_3               3                13
                    V1                     V2                     V3 
             "CN_CNMF"     "METHLYATION_CNMF"          "MIRSEQ_CNMF" 
                    V4 
"MIRSEQ_CHIERARCHICAL" 
> q(save="no")
