
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.4.4139/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.4.4139/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/411540/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/ESCA-TP/3142697/1.GDAC_mergedClustering.Finished/ESCA-TP.transferedmergedcluster.txt", "-fF=ALL", "-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=50, in cluster file=20, common to both=20
[1] "Reduce the number of clustering variables from 30 to 27."
[1] 27 20
[1] "Amp Peak  1(1q42.3)"
[1] 3
      AMP PEAK  1(1Q42.3) CNV AMP PEAK  1(1Q42.3) WILD-TYPE 
                            9                            11 
      AMP PEAK  1(1Q42.3) CNV AMP PEAK  1(1Q42.3) WILD-TYPE 
                            9                            11 
[1] "Amp Peak  2(2p15)"
[1] 3
      AMP PEAK  2(2P15) CNV AMP PEAK  2(2P15) WILD-TYPE 
                         10                          10 
      AMP PEAK  2(2P15) CNV AMP PEAK  2(2P15) WILD-TYPE 
                         10                          10 
[1] "Amp Peak  3(3q28)"
[1] 3
      AMP PEAK  3(3Q28) CNV AMP PEAK  3(3Q28) WILD-TYPE 
                         17                           3 
      AMP PEAK  3(3Q28) CNV AMP PEAK  3(3Q28) WILD-TYPE 
                         17                           3 
[1] "Amp Peak  4(6p12.3)"
[1] 3
      AMP PEAK  4(6P12.3) CNV AMP PEAK  4(6P12.3) WILD-TYPE 
                            6                            14 
      AMP PEAK  4(6P12.3) CNV AMP PEAK  4(6P12.3) WILD-TYPE 
                            6                            14 
[1] "Amp Peak  5(7p11.2)"
[1] 3
      AMP PEAK  5(7P11.2) CNV AMP PEAK  5(7P11.2) WILD-TYPE 
                           12                             8 
      AMP PEAK  5(7P11.2) CNV AMP PEAK  5(7P11.2) WILD-TYPE 
                           12                             8 
[1] "Amp Peak  6(7q31.1)"
[1] 3
      AMP PEAK  6(7Q31.1) CNV AMP PEAK  6(7Q31.1) WILD-TYPE 
                           14                             6 
      AMP PEAK  6(7Q31.1) CNV AMP PEAK  6(7Q31.1) WILD-TYPE 
                           14                             6 
[1] "Amp Peak  8(10p11.21)"
[1] 3
      AMP PEAK  8(10P11.21) CNV AMP PEAK  8(10P11.21) WILD-TYPE 
                              7                              13 
      AMP PEAK  8(10P11.21) CNV AMP PEAK  8(10P11.21) WILD-TYPE 
                              7                              13 
[1] "Amp Peak  9(11p13)"
[1] 3
      AMP PEAK  9(11P13) CNV AMP PEAK  9(11P13) WILD-TYPE 
                           6                           14 
      AMP PEAK  9(11P13) CNV AMP PEAK  9(11P13) WILD-TYPE 
                           6                           14 
[1] "Amp Peak 10(11q13.3)"
[1] 3
      AMP PEAK 10(11Q13.3) CNV AMP PEAK 10(11Q13.3) WILD-TYPE 
                            13                              7 
      AMP PEAK 10(11Q13.3) CNV AMP PEAK 10(11Q13.3) WILD-TYPE 
                            13                              7 
[1] "Amp Peak 11(12p13.33)"
[1] 3
      AMP PEAK 11(12P13.33) CNV AMP PEAK 11(12P13.33) WILD-TYPE 
                             13                               7 
      AMP PEAK 11(12P13.33) CNV AMP PEAK 11(12P13.33) WILD-TYPE 
                             13                               7 
[1] "Amp Peak 12(14q21.3)"
[1] 3
      AMP PEAK 12(14Q21.3) CNV AMP PEAK 12(14Q21.3) WILD-TYPE 
                            11                              9 
      AMP PEAK 12(14Q21.3) CNV AMP PEAK 12(14Q21.3) WILD-TYPE 
                            11                              9 
[1] "Amp Peak 13(18p11.31)"
[1] 3
      AMP PEAK 13(18P11.31) CNV AMP PEAK 13(18P11.31) WILD-TYPE 
                              8                              12 
      AMP PEAK 13(18P11.31) CNV AMP PEAK 13(18P11.31) WILD-TYPE 
                              8                              12 
[1] "Amp Peak 14(Xp21.1)"
[1] 3
      AMP PEAK 14(XP21.1) CNV AMP PEAK 14(XP21.1) WILD-TYPE 
                            6                            14 
      AMP PEAK 14(XP21.1) CNV AMP PEAK 14(XP21.1) WILD-TYPE 
                            6                            14 
[1] "Del Peak  1(2q22.1)"
[1] 3
      DEL PEAK  1(2Q22.1) CNV DEL PEAK  1(2Q22.1) WILD-TYPE 
                            6                            14 
      DEL PEAK  1(2Q22.1) CNV DEL PEAK  1(2Q22.1) WILD-TYPE 
                            6                            14 
[1] "Del Peak  2(3p14.2)"
[1] 3
      DEL PEAK  2(3P14.2) CNV DEL PEAK  2(3P14.2) WILD-TYPE 
                           16                             4 
      DEL PEAK  2(3P14.2) CNV DEL PEAK  2(3P14.2) WILD-TYPE 
                           16                             4 
[1] "Del Peak  4(4q21.23)"
[1] 3
      DEL PEAK  4(4Q21.23) CNV DEL PEAK  4(4Q21.23) WILD-TYPE 
                             9                             11 
      DEL PEAK  4(4Q21.23) CNV DEL PEAK  4(4Q21.23) WILD-TYPE 
                             9                             11 
[1] "Del Peak  5(5q11.2)"
[1] 3
      DEL PEAK  5(5Q11.2) CNV DEL PEAK  5(5Q11.2) WILD-TYPE 
                           11                             9 
      DEL PEAK  5(5Q11.2) CNV DEL PEAK  5(5Q11.2) WILD-TYPE 
                           11                             9 
[1] "Del Peak  6(6p25.3)"
[1] 3
      DEL PEAK  6(6P25.3) CNV DEL PEAK  6(6P25.3) WILD-TYPE 
                            9                            11 
      DEL PEAK  6(6P25.3) CNV DEL PEAK  6(6P25.3) WILD-TYPE 
                            9                            11 
[1] "Del Peak  7(7q31.1)"
[1] 3
      DEL PEAK  7(7Q31.1) CNV DEL PEAK  7(7Q31.1) WILD-TYPE 
                            7                            13 
      DEL PEAK  7(7Q31.1) CNV DEL PEAK  7(7Q31.1) WILD-TYPE 
                            7                            13 
[1] "Del Peak  8(9p21.3)"
[1] 3
      DEL PEAK  8(9P21.3) CNV DEL PEAK  8(9P21.3) WILD-TYPE 
                           17                             3 
      DEL PEAK  8(9P21.3) CNV DEL PEAK  8(9P21.3) WILD-TYPE 
                           17                             3 
[1] "Del Peak  9(10p11.21)"
[1] 3
      DEL PEAK  9(10P11.21) CNV DEL PEAK  9(10P11.21) WILD-TYPE 
                              7                              13 
      DEL PEAK  9(10P11.21) CNV DEL PEAK  9(10P11.21) WILD-TYPE 
                              7                              13 
[1] "Del Peak 10(10q23.31)"
[1] 3
      DEL PEAK 10(10Q23.31) CNV DEL PEAK 10(10Q23.31) WILD-TYPE 
                             10                              10 
      DEL PEAK 10(10Q23.31) CNV DEL PEAK 10(10Q23.31) WILD-TYPE 
                             10                              10 
[1] "Del Peak 11(13q14.2)"
[1] 3
      DEL PEAK 11(13Q14.2) CNV DEL PEAK 11(13Q14.2) WILD-TYPE 
                            11                              9 
      DEL PEAK 11(13Q14.2) CNV DEL PEAK 11(13Q14.2) WILD-TYPE 
                            11                              9 
[1] "Del Peak 12(15q22.2)"
[1] 3
      DEL PEAK 12(15Q22.2) CNV DEL PEAK 12(15Q22.2) WILD-TYPE 
                             5                             15 
      DEL PEAK 12(15Q22.2) CNV DEL PEAK 12(15Q22.2) WILD-TYPE 
                             5                             15 
[1] "Del Peak 13(16q23.1)"
[1] 3
      DEL PEAK 13(16Q23.1) CNV DEL PEAK 13(16Q23.1) WILD-TYPE 
                             7                             13 
      DEL PEAK 13(16Q23.1) CNV DEL PEAK 13(16Q23.1) WILD-TYPE 
                             7                             13 
[1] "Del Peak 15(19q13.31)"
[1] 3
      DEL PEAK 15(19Q13.31) CNV DEL PEAK 15(19Q13.31) WILD-TYPE 
                              8                              12 
      DEL PEAK 15(19Q13.31) CNV DEL PEAK 15(19Q13.31) WILD-TYPE 
                              8                              12 
[1] "Del Peak 16(Xp11.3)"
[1] 3
      DEL PEAK 16(XP11.3) CNV DEL PEAK 16(XP11.3) WILD-TYPE 
                            9                            11 
      DEL PEAK 16(XP11.3) CNV DEL PEAK 16(XP11.3) WILD-TYPE 
                            9                            11 
[1] "data2feature, selection=ALL"
[1] "METHLYATION_CNMF"

Input Data has 1 rows and 20 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "METHLYATION_CNMF"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 20 columns, 0 survival variables, and 1 non-survival variables.
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak  1(1q42.3)
D1V1, multiclass
        clus
vv       AMP PEAK  1(1Q42.3) CNV AMP PEAK  1(1Q42.3) WILD-TYPE
  CLUS_1                       7                             5
  CLUS_2                       2                             3
  CLUS_3                       0                             3

Clustering(2) Variable = Amp Peak  2(2p15)
D2V1, multiclass
        clus
vv       AMP PEAK  2(2P15) CNV AMP PEAK  2(2P15) WILD-TYPE
  CLUS_1                     6                           6
  CLUS_2                     3                           2
  CLUS_3                     1                           2

Clustering(3) Variable = Amp Peak  3(3q28)
D3V1, multiclass
        clus
vv       AMP PEAK  3(3Q28) CNV AMP PEAK  3(3Q28) WILD-TYPE
  CLUS_1                    12                           0
  CLUS_2                     4                           1
  CLUS_3                     1                           2

Clustering(4) Variable = Amp Peak  4(6p12.3)
D4V1, multiclass
        clus
vv       AMP PEAK  4(6P12.3) CNV AMP PEAK  4(6P12.3) WILD-TYPE
  CLUS_1                       4                             8
  CLUS_2                       1                             4
  CLUS_3                       1                             2

Clustering(5) Variable = Amp Peak  5(7p11.2)
D5V1, multiclass
        clus
vv       AMP PEAK  5(7P11.2) CNV AMP PEAK  5(7P11.2) WILD-TYPE
  CLUS_1                       8                             4
  CLUS_2                       1                             4
  CLUS_3                       3                             0

Clustering(6) Variable = Amp Peak  6(7q31.1)
D6V1, multiclass
        clus
vv       AMP PEAK  6(7Q31.1) CNV AMP PEAK  6(7Q31.1) WILD-TYPE
  CLUS_1                       8                             4
  CLUS_2                       3                             2
  CLUS_3                       3                             0

Clustering(7) Variable = Amp Peak  8(10p11.21)
D7V1, multiclass
        clus
vv       AMP PEAK  8(10P11.21) CNV AMP PEAK  8(10P11.21) WILD-TYPE
  CLUS_1                         3                               9
  CLUS_2                         2                               3
  CLUS_3                         2                               1

Clustering(8) Variable = Amp Peak  9(11p13)
D8V1, multiclass
        clus
vv       AMP PEAK  9(11P13) CNV AMP PEAK  9(11P13) WILD-TYPE
  CLUS_1                      3                            9
  CLUS_2                      2                            3
  CLUS_3                      1                            2

Clustering(9) Variable = Amp Peak 10(11q13.3)
D9V1, multiclass
        clus
vv       AMP PEAK 10(11Q13.3) CNV AMP PEAK 10(11Q13.3) WILD-TYPE
  CLUS_1                        9                              3
  CLUS_2                        3                              2
  CLUS_3                        1                              2

Clustering(10) Variable = Amp Peak 11(12p13.33)
D10V1, multiclass
        clus
vv       AMP PEAK 11(12P13.33) CNV AMP PEAK 11(12P13.33) WILD-TYPE
  CLUS_1                         9                               3
  CLUS_2                         4                               1
  CLUS_3                         0                               3

Clustering(11) Variable = Amp Peak 12(14q21.3)
D11V1, multiclass
        clus
vv       AMP PEAK 12(14Q21.3) CNV AMP PEAK 12(14Q21.3) WILD-TYPE
  CLUS_1                        6                              6
  CLUS_2                        2                              3
  CLUS_3                        3                              0

Clustering(12) Variable = Amp Peak 13(18p11.31)
D12V1, multiclass
        clus
vv       AMP PEAK 13(18P11.31) CNV AMP PEAK 13(18P11.31) WILD-TYPE
  CLUS_1                         4                               8
  CLUS_2                         3                               2
  CLUS_3                         1                               2

Clustering(13) Variable = Amp Peak 14(Xp21.1)
D13V1, multiclass
        clus
vv       AMP PEAK 14(XP21.1) CNV AMP PEAK 14(XP21.1) WILD-TYPE
  CLUS_1                       3                             9
  CLUS_2                       2                             3
  CLUS_3                       1                             2

Clustering(14) Variable = Del Peak  1(2q22.1)
D14V1, multiclass
        clus
vv       DEL PEAK  1(2Q22.1) CNV DEL PEAK  1(2Q22.1) WILD-TYPE
  CLUS_1                       4                             8
  CLUS_2                       1                             4
  CLUS_3                       1                             2

Clustering(15) Variable = Del Peak  2(3p14.2)
D15V1, multiclass
        clus
vv       DEL PEAK  2(3P14.2) CNV DEL PEAK  2(3P14.2) WILD-TYPE
  CLUS_1                      10                             2
  CLUS_2                       4                             1
  CLUS_3                       2                             1

Clustering(16) Variable = Del Peak  4(4q21.23)
D16V1, multiclass
        clus
vv       DEL PEAK  4(4Q21.23) CNV DEL PEAK  4(4Q21.23) WILD-TYPE
  CLUS_1                        7                              5
  CLUS_2                        1                              4
  CLUS_3                        1                              2

Clustering(17) Variable = Del Peak  5(5q11.2)
D17V1, multiclass
        clus
vv       DEL PEAK  5(5Q11.2) CNV DEL PEAK  5(5Q11.2) WILD-TYPE
  CLUS_1                      10                             2
  CLUS_2                       0                             5
  CLUS_3                       1                             2

Clustering(18) Variable = Del Peak  6(6p25.3)
D18V1, multiclass
        clus
vv       DEL PEAK  6(6P25.3) CNV DEL PEAK  6(6P25.3) WILD-TYPE
  CLUS_1                       6                             6
  CLUS_2                       1                             4
  CLUS_3                       2                             1

Clustering(19) Variable = Del Peak  7(7q31.1)
D19V1, multiclass
        clus
vv       DEL PEAK  7(7Q31.1) CNV DEL PEAK  7(7Q31.1) WILD-TYPE
  CLUS_1                       4                             8
  CLUS_2                       1                             4
  CLUS_3                       2                             1

Clustering(20) Variable = Del Peak  8(9p21.3)
D20V1, multiclass
        clus
vv       DEL PEAK  8(9P21.3) CNV DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                      10                             2
  CLUS_2                       5                             0
  CLUS_3                       2                             1

Clustering(21) Variable = Del Peak  9(10p11.21)
D21V1, multiclass
        clus
vv       DEL PEAK  9(10P11.21) CNV DEL PEAK  9(10P11.21) WILD-TYPE
  CLUS_1                         7                               5
  CLUS_2                         0                               5
  CLUS_3                         0                               3

Clustering(22) Variable = Del Peak 10(10q23.31)
D22V1, multiclass
        clus
vv       DEL PEAK 10(10Q23.31) CNV DEL PEAK 10(10Q23.31) WILD-TYPE
  CLUS_1                         7                               5
  CLUS_2                         2                               3
  CLUS_3                         1                               2

Clustering(23) Variable = Del Peak 11(13q14.2)
D23V1, multiclass
        clus
vv       DEL PEAK 11(13Q14.2) CNV DEL PEAK 11(13Q14.2) WILD-TYPE
  CLUS_1                        9                              3
  CLUS_2                        2                              3
  CLUS_3                        0                              3

Clustering(24) Variable = Del Peak 12(15q22.2)
D24V1, multiclass
        clus
vv       DEL PEAK 12(15Q22.2) CNV DEL PEAK 12(15Q22.2) WILD-TYPE
  CLUS_1                        3                              9
  CLUS_2                        2                              3
  CLUS_3                        0                              3

Clustering(25) Variable = Del Peak 13(16q23.1)
D25V1, multiclass
        clus
vv       DEL PEAK 13(16Q23.1) CNV DEL PEAK 13(16Q23.1) WILD-TYPE
  CLUS_1                        3                              9
  CLUS_2                        2                              3
  CLUS_3                        2                              1

Clustering(26) Variable = Del Peak 15(19q13.31)
D26V1, multiclass
        clus
vv       DEL PEAK 15(19Q13.31) CNV DEL PEAK 15(19Q13.31) WILD-TYPE
  CLUS_1                         5                               7
  CLUS_2                         2                               3
  CLUS_3                         1                               2

Clustering(27) Variable = Del Peak 16(Xp11.3)
D27V1, multiclass
        clus
vv       DEL PEAK 16(XP11.3) CNV DEL PEAK 16(XP11.3) WILD-TYPE
  CLUS_1                       5                             7
  CLUS_2                       3                             2
  CLUS_3                       1                             2
                V1 
"METHLYATION_CNMF" 
> q(save="no")
