From noreply at r-forge.r-project.org Wed Feb 13 14:14:27 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 13 Feb 2013 14:14:27 +0100 (CET) Subject: [Patchwork-commits] r161 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/inst/perl pkg/patchwork/inst/python Message-ID: <20130213131427.A9704184B71@r-forge.r-project.org> Author: sebastian_d Date: 2013-02-13 14:14:27 +0100 (Wed, 13 Feb 2013) New Revision: 161 Modified: .git/COMMIT_EDITMSG .git/index .git/logs/HEAD .git/logs/refs/heads/master .git/logs/refs/remotes/origin/master .git/refs/heads/master .git/refs/remotes/origin/master pkg/patchwork/inst/perl/pile2alleles.pl pkg/patchwork/inst/python/Pysamloader.py Log: Updated error handling for pile2alleles Modified: .git/COMMIT_EDITMSG =================================================================== --- .git/COMMIT_EDITMSG 2013-01-31 11:22:11 UTC (rev 160) +++ .git/COMMIT_EDITMSG 2013-02-13 13:14:27 UTC (rev 161) @@ -1 +1 @@ -updates size of cex for karyotype plot to make the small pictures more interpretable +Updated error handling in pile2alleles Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2013-01-31 11:22:11 UTC (rev 160) +++ .git/logs/HEAD 2013-02-13 13:14:27 UTC (rev 161) @@ -28,3 +28,5 @@ c39f1b06a56367684e8062040df7214da6a79455 8d49ce11a9941d73d7be44948f908a139958e029 Sebastian DiLorenzo 1358776614 +0100 commit: minor update 8d49ce11a9941d73d7be44948f908a139958e029 4577fee5ce0968b311fa252e9df8fba284522e5d Sebastian DiLorenzo 1358869240 +0100 commit: removed antique from bugfixing in patchworkCG 4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable +a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge +acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761388 +0100 commit: Updated error handling in pile2alleles Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2013-01-31 11:22:11 UTC (rev 160) +++ .git/logs/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161) @@ -28,3 +28,5 @@ c39f1b06a56367684e8062040df7214da6a79455 8d49ce11a9941d73d7be44948f908a139958e029 Sebastian DiLorenzo 1358776614 +0100 commit: minor update 8d49ce11a9941d73d7be44948f908a139958e029 4577fee5ce0968b311fa252e9df8fba284522e5d Sebastian DiLorenzo 1358869240 +0100 commit: removed antique from bugfixing in patchworkCG 4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable +a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge +acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761388 +0100 commit: Updated error handling in pile2alleles Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2013-01-31 11:22:11 UTC (rev 160) +++ .git/logs/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161) @@ -28,3 +28,5 @@ c39f1b06a56367684e8062040df7214da6a79455 8d49ce11a9941d73d7be44948f908a139958e029 Sebastian DiLorenzo 1358776628 +0100 update by push 8d49ce11a9941d73d7be44948f908a139958e029 4577fee5ce0968b311fa252e9df8fba284522e5d Sebastian DiLorenzo 1358869254 +0100 update by push 4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo 1359037348 +0100 update by push +a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631524 +0100 update by push +acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761405 +0100 update by push Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2013-01-31 11:22:11 UTC (rev 160) +++ .git/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161) @@ -1 +1 @@ -a75b0350402a356de4d9991f66d7fd1bc785a46f +f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2013-01-31 11:22:11 UTC (rev 160) +++ .git/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161) @@ -1 +1 @@ -a75b0350402a356de4d9991f66d7fd1bc785a46f +f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Modified: pkg/patchwork/inst/perl/pile2alleles.pl =================================================================== --- pkg/patchwork/inst/perl/pile2alleles.pl 2013-01-31 11:22:11 UTC (rev 160) +++ pkg/patchwork/inst/perl/pile2alleles.pl 2013-02-13 13:14:27 UTC (rev 161) @@ -32,44 +32,51 @@ $iupac{'T'}{'S'} = 'G|C'; $iupac{'T'}{'M'} = 'A|C'; - while () { chomp; - my ($chr, $pos, $ref, $cons, $consQual, $depth, $baseString) = (split /\t/, $_)[0,1,2,3,4,7,8]; - $ref = uc $ref; - if ($ref eq '*'){next;} - if ($cons eq 'N'){next;} - my $snp = ($cons =~ m/[AGCT]/) ? $cons : $iupac{$ref}{$cons}; - $snps{$chr}{$pos}{'ref'} = $ref; - $snps{$chr}{$pos}{'snp'} = $snp; - $snps{$chr}{$pos}{'qual'} = $consQual; - my $snpCount; - if ($snps{$chr}{$pos}{'snp'} eq 'A') { - $snpCount = $baseString =~ tr/Aa/Aa/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'C') { - $snpCount = $baseString =~ tr/Cc/Cc/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'G') { - $snpCount = $baseString =~ tr/Gg/Gg/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'T') { - $snpCount = $baseString =~ tr/Tt/Tt/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|C') { - $snpCount = $baseString =~ tr/AaCc/AaCc/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|G') { - $snpCount = $baseString =~ tr/AaGg/AaGg/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|T') { - $snpCount = $baseString =~ tr/AaTt/AaTt/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|C') { - $snpCount = $baseString =~ tr/GgCc/GgCc/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|T') { - $snpCount = $baseString =~ tr/GgTt/GgTt/; - } elsif ($snps{$chr}{$pos}{'snp'} eq 'C|T') { - $snpCount = $baseString =~ tr/CcTt/CcTt/; - } else { - $snpCount = 0; + #if ($_ == ""){next;} + if ($_ =~ /(\S+)\t(\S+)\t(\S+)\t(\S+)\t(\S+)\t\S+\t\S+\t(\S+)\t(\S+)\t\S+/) + { + my ($chr, $pos, $ref, $cons, $consQual, $depth, $baseString) = ($1,$2,$3,$4,$5,$6,$7); #(split /\t/, $_)[0,1,2,3,4,7,8]; + $ref = uc $ref; + if ($ref eq '*'){next;} + if ($cons eq 'N'){next;} + my $snp = ($cons =~ m/[AGCT]/) ? $cons : $iupac{$ref}{$cons}; + $snps{$chr}{$pos}{'ref'} = $ref; + $snps{$chr}{$pos}{'snp'} = $snp; + $snps{$chr}{$pos}{'qual'} = $consQual; + my $snpCount; + if ($snps{$chr}{$pos}{'snp'} eq 'A') { + $snpCount = $baseString =~ tr/Aa/Aa/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'C') { + $snpCount = $baseString =~ tr/Cc/Cc/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'G') { + $snpCount = $baseString =~ tr/Gg/Gg/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'T') { + $snpCount = $baseString =~ tr/Tt/Tt/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|C') { + $snpCount = $baseString =~ tr/AaCc/AaCc/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|G') { + $snpCount = $baseString =~ tr/AaGg/AaGg/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|T') { + $snpCount = $baseString =~ tr/AaTt/AaTt/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|C') { + $snpCount = $baseString =~ tr/GgCc/GgCc/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|T') { + $snpCount = $baseString =~ tr/GgTt/GgTt/; + } elsif ($snps{$chr}{$pos}{'snp'} eq 'C|T') { + $snpCount = $baseString =~ tr/CcTt/CcTt/; + } else { + $snpCount = 0; + } + $snps{$chr}{$pos}{'depth'} = $depth; + $snps{$chr}{$pos}{'freq'} = $snpCount; + $snps{$chr}{$pos}{'pct'} = sprintf '%.2f', ($snpCount/$depth); + } + else + { + print STDERR "Line incompatible: $_ \n"; } - $snps{$chr}{$pos}{'depth'} = $depth; - $snps{$chr}{$pos}{'freq'} = $snpCount; - $snps{$chr}{$pos}{'pct'} = sprintf '%.2f', ($snpCount/$depth); } Modified: pkg/patchwork/inst/python/Pysamloader.py =================================================================== --- pkg/patchwork/inst/python/Pysamloader.py 2013-01-31 11:22:11 UTC (rev 160) +++ pkg/patchwork/inst/python/Pysamloader.py 2013-02-13 13:14:27 UTC (rev 161) @@ -4,10 +4,12 @@ import pysam +filename = sys.argv[1] + try: infile = pysam.Samfile(sys.argv[1],"rb") except IOError,eStr: - print "Error:Cannot open",infile," for reading: ", eStr + print "Error:Cannot open ",filename," for reading: ", eStr sys.exit() outfile = open(".Tmp_chr_pos","w") From noreply at r-forge.r-project.org Thu Feb 14 11:33:21 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 14 Feb 2013 11:33:21 +0100 (CET) Subject: [Patchwork-commits] r162 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R www Message-ID: <20130214103321.BD9DB183A3C@r-forge.r-project.org> Author: sebastian_d Date: 2013-02-14 11:33:21 +0100 (Thu, 14 Feb 2013) New Revision: 162 Modified: .git/COMMIT_EDITMSG .git/index .git/logs/HEAD .git/logs/refs/heads/master .git/logs/refs/remotes/origin/master .git/refs/heads/master .git/refs/remotes/origin/master pkg/patchwork/R/patchwork.plot.r www/changelog.php Log: Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information Modified: .git/COMMIT_EDITMSG =================================================================== --- .git/COMMIT_EDITMSG 2013-02-13 13:14:27 UTC (rev 161) +++ .git/COMMIT_EDITMSG 2013-02-14 10:33:21 UTC (rev 162) @@ -1 +1 @@ -Updated error handling in pile2alleles +Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2013-02-13 13:14:27 UTC (rev 161) +++ .git/logs/HEAD 2013-02-14 10:33:21 UTC (rev 162) @@ -30,3 +30,4 @@ 4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761388 +0100 commit: Updated error handling in pile2alleles +f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo 1360838155 +0100 commit: Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161) +++ .git/logs/refs/heads/master 2013-02-14 10:33:21 UTC (rev 162) @@ -30,3 +30,4 @@ 4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761388 +0100 commit: Updated error handling in pile2alleles +f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo 1360838155 +0100 commit: Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161) +++ .git/logs/refs/remotes/origin/master 2013-02-14 10:33:21 UTC (rev 162) @@ -30,3 +30,4 @@ 4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo 1359037348 +0100 update by push a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631524 +0100 update by push acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761405 +0100 update by push +f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo 1360838170 +0100 update by push Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161) +++ .git/refs/heads/master 2013-02-14 10:33:21 UTC (rev 162) @@ -1 +1 @@ -f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 +ae581e53647259304439e470cd67db340b07cb35 Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161) +++ .git/refs/remotes/origin/master 2013-02-14 10:33:21 UTC (rev 162) @@ -1 +1 @@ -f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 +ae581e53647259304439e470cd67db340b07cb35 Modified: pkg/patchwork/R/patchwork.plot.r =================================================================== --- pkg/patchwork/R/patchwork.plot.r 2013-02-13 13:14:27 UTC (rev 161) +++ pkg/patchwork/R/patchwork.plot.r 2013-02-14 10:33:21 UTC (rev 162) @@ -65,6 +65,12 @@ if (!is.null(normalalf)) { + ## Extract somatic variants + normaltemp=data.frame(achr=normalalf$achr,apos=normalalf$apos,normal=T) + somatic <- merge(normaltemp,alf,by=1:2,all.x=F, all.y=T) + somatic <- somatic[is.na(somatic$normal),] + save(somatic,file=paste(name,"_somatic.Rdata",sep="")) + ## Remove all but the heterozygous SNPs normalalf <- normalalf[normalalf$amin/normalalf$atot > 0.2,] alf <- merge(normalalf[,1:2],alf,by=1:2,all=F) } Modified: www/changelog.php =================================================================== --- www/changelog.php 2013-02-13 13:14:27 UTC (rev 161) +++ www/changelog.php 2013-02-14 10:33:21 UTC (rev 162) @@ -5,6 +5,14 @@ Here you can find the recent changes made to the patchwork and patchworkCG packages.
+ +
Homepage -
From noreply at r-forge.r-project.org Fri Feb 22 09:57:16 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 22 Feb 2013 09:57:16 +0100 (CET) Subject: [Patchwork-commits] r163 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin www Message-ID: <20130222085716.22A29184870@r-forge.r-project.org> Author: sebastian_d Date: 2013-02-22 09:57:15 +0100 (Fri, 22 Feb 2013) New Revision: 163 Modified: .git/COMMIT_EDITMSG .git/index .git/logs/HEAD .git/logs/refs/heads/master .git/logs/refs/remotes/origin/master .git/refs/heads/master .git/refs/remotes/origin/master www/AI_Cov.php www/pw_exec.php www/pw_requ.php www/pw_resu.php Log: some changes to homepage due to feedback from alexey Modified: .git/COMMIT_EDITMSG =================================================================== --- .git/COMMIT_EDITMSG 2013-02-14 10:33:21 UTC (rev 162) +++ .git/COMMIT_EDITMSG 2013-02-22 08:57:15 UTC (rev 163) @@ -1 +1 @@ -Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information +some homepage updates from alexeys feedback Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2013-02-14 10:33:21 UTC (rev 162) +++ .git/logs/HEAD 2013-02-22 08:57:15 UTC (rev 163) @@ -31,3 +31,4 @@ a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761388 +0100 commit: Updated error handling in pile2alleles f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo 1360838155 +0100 commit: Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information +ae581e53647259304439e470cd67db340b07cb35 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Sebastian DiLorenzo 1361523526 +0100 commit: some homepage updates from alexeys feedback Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2013-02-14 10:33:21 UTC (rev 162) +++ .git/logs/refs/heads/master 2013-02-22 08:57:15 UTC (rev 163) @@ -31,3 +31,4 @@ a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761388 +0100 commit: Updated error handling in pile2alleles f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo 1360838155 +0100 commit: Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information +ae581e53647259304439e470cd67db340b07cb35 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Sebastian DiLorenzo 1361523526 +0100 commit: some homepage updates from alexeys feedback Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2013-02-14 10:33:21 UTC (rev 162) +++ .git/logs/refs/remotes/origin/master 2013-02-22 08:57:15 UTC (rev 163) @@ -31,3 +31,4 @@ a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo 1359631524 +0100 update by push acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo 1360761405 +0100 update by push f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo 1360838170 +0100 update by push +ae581e53647259304439e470cd67db340b07cb35 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Sebastian DiLorenzo 1361523599 +0100 update by push Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2013-02-14 10:33:21 UTC (rev 162) +++ .git/refs/heads/master 2013-02-22 08:57:15 UTC (rev 163) @@ -1 +1 @@ -ae581e53647259304439e470cd67db340b07cb35 +2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2013-02-14 10:33:21 UTC (rev 162) +++ .git/refs/remotes/origin/master 2013-02-22 08:57:15 UTC (rev 163) @@ -1 +1 @@ -ae581e53647259304439e470cd67db340b07cb35 +2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Modified: www/AI_Cov.php =================================================================== --- www/AI_Cov.php 2013-02-14 10:33:21 UTC (rev 162) +++ www/AI_Cov.php 2013-02-22 08:57:15 UTC (rev 163) @@ -182,7 +182,7 @@ Coverage is measured as total DNA content and normalized around 1. You will get a clearer picture at higher coverage data, 120x etc, however patchworkCG has high quality results - with low coverage aswell. + with low coverage as well.
Modified: www/pw_exec.php =================================================================== --- www/pw_exec.php 2013-02-14 10:33:21 UTC (rev 162) +++ www/pw_exec.php 2013-02-22 08:57:15 UTC (rev 163) @@ -10,10 +10,12 @@ whole-genome sequenced data of tumors.

It is recommended that you run patchwork from a "clean" working directory to avoid the risk - of having files write over eachother if you run multiple different samples.

+ of having files overwrite in the case of running patchwork on multiple samples.

Execution may take quite a while depending on the size of your sample, -if possible run it on a dedicated computer.

+if possible run it on a dedicated computer. (A 50GB tumor sample with a matched 50GB normal sample took ~6 hours +and used 10GB (out of 24GB available) RAM. However +there are many factors that influence runtime so be generous with time/RAM allocation!)

Initiate the R environment and load the patchwork and patchworkData libraries:
@@ -236,8 +238,8 @@

patchwork.copynumbers()

- The function patchwork.copynumbers() determines which relationship between coverage - and allelic imbalance signifies what copy number and allele ratio for each segment.

+ The function patchwork.copynumbers() uses the relationship between coverage + and allelic imbalance to assign copy number and allele ratio for each segment.

The only file you absolutely must have in your working for the next part of execution is (prefix)_copynumbers.Rdata.

@@ -284,7 +286,7 @@ To infer the arguments for patchwork.copynumbers() you will need to look at one of the chromosomal plots generated using patchwork.plot(). The structure and relationships in the plot can be interpreted -to figure out the most probable location the allele-specific copynumbers.

+to figure out the most probable locations of the allele-specific copynumbers.

For information to help you understand the axis, allelic imbalance and coverage, and layout of the plot click here. Modified: www/pw_requ.php =================================================================== --- www/pw_requ.php 2013-02-14 10:33:21 UTC (rev 162) +++ www/pw_requ.php 2013-02-22 08:57:15 UTC (rev 163) @@ -30,7 +30,7 @@ files. There is really no point in using all of them.

If you have a matched normal sample you should make a pileup of this and use those two arguments. -If you have a normal you should also create a BAI file of it, it will not be a parameter but is +You should also create a BAI file of it, it will not be a parameter but is required for the file to be read by patchwork.
In some cases it may be better to use the reference file and a pileup. @@ -65,11 +65,11 @@
  • Aligned using same reference genome (HG18/HG19)
  • They should be sequenced using the same technique
  • They should be from the same organism
    • -
  • They should be non-tumerous
    • +
  • They should be non-tumorous
  • They should be same sex
    • -It is recommended that you use atleast 3 BAM files to create your reference. +It is recommended that you use at least 3 BAM files to create your reference. Note also that if your tumor sample is from a different sex than your reference samples you may not get optimal results. There is a paramter in the second part of analysis, patchwork.copynumbers(), to correct for this however if you are interested specifically in the sex chromosomes we would definitely recommend using the same sex in reference as in tumor sample. Modified: www/pw_resu.php =================================================================== --- www/pw_resu.php 2013-02-14 10:33:21 UTC (rev 162) +++ www/pw_resu.php 2013-02-22 08:57:15 UTC (rev 163) @@ -1,7 +1,7 @@

    Plots of patchwork.plot()

    After running patchwork.plot() you should have 24 plots in your working directory similar -to the example plot below, one for each chromosome.

    +to the example plot below, one for each chromosome and two overviews.

    For information regarding allelic imbalance and coverage click here. @@ -39,12 +39,13 @@


    -The far left tiny cluster, on Coverage axis, is the deletions, copy number 1. +Far left on the Coverage axis is a small cluster. As it has the lowest coverage in the sample and is a single cluster +seen in allelic imbalance perspective it is copy number 1. Moving to the right the next two clusters, lower cluster is quite small, are the allelic states of copy number 2. Following this reasoning the next set of clusters must be copy number 3, then 4 etc. The average copy number for the sample is just above 3. -This arrangement of the genome is easier to see from one of the plots generated by +This arrangement of the genome is labeled farther down in one of the plots generated by patchwork.copynumbers() or in our section above on allelic imbalance, however before using that function you will need to be able to determine the constitution of the tumor genome as it is used as input arguments for patchwork.copynumbers()! @@ -83,7 +84,7 @@ And so on.

    The other chromosomal plots generated from patchwork.copynumbers() are the same as -the ones generated by patchwork.plot() but with one extra part of the plot.
    +the ones generated by patchwork.plot() but with one extra part of the plot, discussed below.