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Question: Gviz problem to extract some track with UcscTrack like Broad ChromHMM
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gravatar for florian.hahne@novartis.com
4.3 years ago by
Switzerland
Hi Martin, I'd really like to help, but from you code below I can't tell for which genome you are trying to do this (the value of 'gen'). I also have no idea how you came up with the 'track.name' vector. In general, Gviz is using rtracklayer::tableNames to figure out which tables and tracks are available. So you should get the same results, assuming that you checked for the same chromosome. Also please always include the output of sessionInfo() when asking for help in order for us to know which R and package version we are dealing with. Florian From: <martin>, Tiphaine <tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk>> Date: Thursday, February 13, 2014 11:18 PM To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Subject: Gviz problem to extract some track with UcscTrack like Broad ChromHMM Dear Florian, I am trying to use your package Gviz to visualise my data and some data from UCSC, for example: "Broad ChromHMM”. But I have a error message. I don’t understand because I have checked with the package rtracklayer, whose your package inherits, the name of tracks and tables. Could you help me ? Regards Tiph R Command used to find the name of track and table >track.names["Broad ChromHMM"] Broad ChromHMM “wgEncodeBroadHmm" >sapply(track, function(track) { + tableNames(ucscTableQuery(mySession, track=track)) + }) Broad ChromHMM [1,] "wgEncodeBroadHmmGm12878HMM" [2,] "wgEncodeBroadHmmH1hescHMM" [3,] "wgEncodeBroadHmmK562HMM" [4,] "wgEncodeBroadHmmHepg2HMM" [5,] "wgEncodeBroadHmmHuvecHMM" [6,] "wgEncodeBroadHmmHmecHMM" [7,] "wgEncodeBroadHmmHsmmHMM" [8,] "wgEncodeBroadHmmNhekHMM" [9,] "wgEncodeBroadHmmNhlfHMM" > UcscTrack(genome = gen, chrom My errors when I try to use UcscTrack: > UcscTrack(genome = gen, chromosome = chr, track = "Broad ChromHMM", + table="wgEncodeBroadHmmGm12878HMM", + from = start, to = end, trackType = "AnnotationTrack", + rstarts = "chromStart", rends = "chromEnd", gene = "name", + symbol = "name", strand = "strand", + fill = "itemRgb", name = "UCSC Genes”) Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : 'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv > UcscTrack(genome = gen, chromosome = chr, track = "wgEncodeBroadHmm", + table="wgEncodeBroadHmmGm12878HMM", + from = start, to = end, trackType = "AnnotationTrack", + rstarts = "chromStart", rends = "chromEnd", gene = "name", + symbol = "name", strand = "strand", + fill = "itemRgb", name = "UCSC Genes”) Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : 'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by florian.hahne@novartis.com1.6k
0
gravatar for florian.hahne@novartis.com
4.3 years ago by
Switzerland
Hi Martin, This seems to be a problem in the rtracklayer package: > library(rtracklayer) > session <- browserSession() > genome(session) <- "hg19" > grep("Broad", trackNames(session)) integer(0) > grep("Broad", names(trackNames(session))) integer(0) But: > query <- ucscTableQuery(session, "Broad ChromHMM") > tableNames(query) [1] "wgEncodeBroadHmmGm12878HMM" "wgEncodeBroadHmmH1hescHMM" [3] "wgEncodeBroadHmmK562HMM" "wgEncodeBroadHmmHepg2HMM" [5] "wgEncodeBroadHmmHuvecHMM" "wgEncodeBroadHmmHmecHMM" [7] "wgEncodeBroadHmmHsmmHMM" "wgEncodeBroadHmmNhekHMM" [9] "wgEncodeBroadHmmNhlfHMM" Even though the Broad ChromHMM track exists, it is not listed by trackNames(). The output of trackNames is used by Gviz to check whether the requested track exists in order to give a more useful error message. As a quick fix for now you could simply download the track data via rtracklayer into a GRanges object and use that as the input for your AnnotationTrack() constructor. Michael, is that a bug in rtracklayer, or is it intentional that trackNames does not list all available tracks? Broad ChromHMM is also listed in the table browser: http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=363821417&clade=mammal&o rg=Human&db=hg19&hgta_group=allTracks&hgta_track=wgEncodeBroadHmm&hgta _table=0&hgta_regionType=range&position=chr21%3A33%2C031%2C597-33%2C04 1%2C570&hgta_outputType=bed&hgta_outFileName= > sessionInfo() R version 3.0.2 Patched (2013-10-27 r64116) Platform: i386-apple-darwin12.5.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools parallel grid stats graphics grDevices utils [8] datasets methods base other attached packages: [1] rtracklayer_1.22.0 GenomicRanges_1.14.4 XVector_0.2.0 [4] IRanges_1.20.6 Biobase_2.22.0 BiocGenerics_0.8.0 [7] Gviz_1.6.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.24.0 biomaRt_2.18.0 Biostrings_2.30.1 [4] biovizBase_1.10.7 bitops_1.0-6 BSgenome_1.30.0 [7] cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 [10] dichromat_2.0-0 Formula_1.1-1 GenomicFeatures_1.14.2 [13] Hmisc_3.13-0 labeling_0.2 lattice_0.20-24 [16] latticeExtra_0.6-26 munsell_0.4.2 plyr_1.8 [19] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.14.2 [22] RSQLite_0.11.4 scales_0.2.3 splines_3.0.2 [25] stats4_3.0.2 stringr_0.6.2 survival_2.37-4 [28] XML_3.98-1.1 zlibbioc_1.8.0 Florian Hi, My genome is hg19 and I try to have the list of tables related to track "Broad ChromHMM ". I used the command line from rtracklayer to create the vector of potential tables. I put my sessionInfo(). Sorry to have forgotten to give you it. Also, I don't know if I am alone in this situation but when I read your documentation from web navigator (safari or firefox) or preview in mac OS X 10.6, I don't see the picture. Regards, Tiphaine On 17/02/14 08:31, Hahne, Florian wrote: Hi Martin, I'd really like to help, but from you code below I can't tell for which genome you are trying to do this (the value of 'gen'). I also have no idea how you came up with the 'track.name' vector. In general, Gviz is using rtracklayer::tableNames to figure out which tables and tracks are available. So you should get the same results, assuming that you checked for the same chromosome. Also please always include the output of sessionInfo() when asking for help in order for us to know which R and package version we are dealing with. Florian From: <martin>, Tiphaine <tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk>> Date: Thursday, February 13, 2014 11:18 PM To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Subject: Gviz problem to extract some track with UcscTrack like Broad ChromHMM Dear Florian, I am trying to use your package Gviz to visualise my data and some data from UCSC, for example: "Broad ChromHMM”. But I have a error message. I don’t understand because I have checked with the package rtracklayer, whose your package inherits, the name of tracks and tables. Could you help me ? Regards Tiph R Command used to find the name of track and table >track.names["Broad ChromHMM"] Broad ChromHMM “wgEncodeBroadHmm" >sapply(track, function(track) { + tableNames(ucscTableQuery(mySession, track=track)) + }) Broad ChromHMM [1,] "wgEncodeBroadHmmGm12878HMM" [2,] "wgEncodeBroadHmmH1hescHMM" [3,] "wgEncodeBroadHmmK562HMM" [4,] "wgEncodeBroadHmmHepg2HMM" [5,] "wgEncodeBroadHmmHuvecHMM" [6,] "wgEncodeBroadHmmHmecHMM" [7,] "wgEncodeBroadHmmHsmmHMM" [8,] "wgEncodeBroadHmmNhekHMM" [9,] "wgEncodeBroadHmmNhlfHMM" > UcscTrack(genome = gen, chrom My errors when I try to use UcscTrack: > UcscTrack(genome = gen, chromosome = chr, track = "Broad ChromHMM", + table="wgEncodeBroadHmmGm12878HMM", + from = start, to = end, trackType = "AnnotationTrack", + rstarts = "chromStart", rends = "chromEnd", gene = "name", + symbol = "name", strand = "strand", + fill = "itemRgb", name = "UCSC Genes”) Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : 'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv > UcscTrack(genome = gen, chromosome = chr, track = "wgEncodeBroadHmm", + table="wgEncodeBroadHmmGm12878HMM", + from = start, to = end, trackType = "AnnotationTrack", + rstarts = "chromStart", rends = "chromEnd", gene = "name", + symbol = "name", strand = "strand", + fill = "itemRgb", name = "UCSC Genes”) Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : 'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv -- ---------------------------- Tiphaine Martin PhD Research Student | King's College The Department of Twin Research & Genetic Epidemiology Genetics & Molecular Medicine Division St Thomas' Hospital 4th Floor, Block D, South Wing SE1 7EH London United Kingdom email : tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk> Fax: +44 (0) 207 188 6761 [[alternative HTML version deleted]]
ADD COMMENTlink written 4.3 years ago by florian.hahne@novartis.com1.6k
Hi Florian, trackNames,UCSCSession will only return the tracks in the actual browser. To get the track names from the table browser, just use trackNames,UCSCTableQuery. In other words, UCSCTableQuery is the interface to the table browser, while UCSCSession is the interface to the actual browser. Michael On Fri, Feb 21, 2014 at 1:40 AM, Hahne, Florian <florian.hahne@novartis.com>wrote: > Hi Martin, > This seems to be a problem in the rtracklayer package: > > > library(rtracklayer) > > session <- browserSession() > > genome(session) <- "hg19" > > > grep("Broad", trackNames(session)) > integer(0) > > > grep("Broad", names(trackNames(session))) > integer(0) > > But: > > query <- ucscTableQuery(session, "Broad ChromHMM") > > tableNames(query) > [1] "wgEncodeBroadHmmGm12878HMM" "wgEncodeBroadHmmH1hescHMM" > [3] "wgEncodeBroadHmmK562HMM" "wgEncodeBroadHmmHepg2HMM" > [5] "wgEncodeBroadHmmHuvecHMM" "wgEncodeBroadHmmHmecHMM" > [7] "wgEncodeBroadHmmHsmmHMM" "wgEncodeBroadHmmNhekHMM" > [9] "wgEncodeBroadHmmNhlfHMM" > > Even though the Broad ChromHMM track exists, it is not listed > by trackNames(). The output of trackNames is used by Gviz to check whether > the requested track exists in order to give a more useful error message. As > a quick fix for now you could simply download the track data via > rtracklayer into a GRanges object and use that as the input for your > AnnotationTrack() constructor. > > Michael, is that a bug in rtracklayer, or is it intentional that > trackNames does not list all available tracks? Broad ChromHMM is also > listed in the table browser: > > http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=363821417&clade=mammal &org=Human&db=hg19&hgta_group=allTracks&hgta_track=wgEncodeBroadHmm&hg ta_table=0&hgta_regionType=range&position=chr21%3A33%2C031%2C597-33%2C 041%2C570&hgta_outputType=bed&hgta_outFileName= > > > sessionInfo() > R version 3.0.2 Patched (2013-10-27 r64116) > Platform: i386-apple-darwin12.5.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools parallel grid stats graphics grDevices utils > [8] datasets methods base > > other attached packages: > [1] rtracklayer_1.22.0 GenomicRanges_1.14.4 XVector_0.2.0 > [4] IRanges_1.20.6 Biobase_2.22.0 BiocGenerics_0.8.0 > [7] Gviz_1.6.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.24.0 biomaRt_2.18.0 Biostrings_2.30.1 > [4] biovizBase_1.10.7 bitops_1.0-6 BSgenome_1.30.0 > [7] cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 > [10] dichromat_2.0-0 Formula_1.1-1 GenomicFeatures_1.14.2 > [13] Hmisc_3.13-0 labeling_0.2 lattice_0.20-24 > [16] latticeExtra_0.6-26 munsell_0.4.2 plyr_1.8 > [19] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.14.2 > [22] RSQLite_0.11.4 scales_0.2.3 splines_3.0.2 > [25] stats4_3.0.2 stringr_0.6.2 survival_2.37-4 > [28] XML_3.98-1.1 zlibbioc_1.8.0 > > Florian > > > > > > Hi, > > My genome is hg19 and I try to have the list of tables related to track "Broad > ChromHMM ". I used the command line from rtracklayer to create the vector > of potential tables. > > I put my sessionInfo(). Sorry to have forgotten to give you it. > > Also, I don't know if I am alone in this situation but when I read your > documentation from web navigator (safari or firefox) or preview in mac OS X > 10.6, I don't see the picture. > > Regards, > Tiphaine > > On 17/02/14 08:31, Hahne, Florian wrote: > > Hi Martin, > I'd really like to help, but from you code below I can't tell for which > genome you are trying to do this (the value of 'gen'). I also have no idea > how you came up with the 'track.name' vector. > In general, Gviz is using rtracklayer::tableNames to figure out which > tables and tracks are available. So you should get the same results, > assuming that you checked for the same chromosome. > Also please always include the output of sessionInfo() when asking for > help in order for us to know which R and package version we are dealing > with. > Florian > > From: <martin>, Tiphaine <tiphaine.martin@kcl.ac.uk> > Date: Thursday, February 13, 2014 11:18 PM > To: Florian Hahne <florian.hahne@novartis.com> > Subject: Gviz problem to extract some track with UcscTrack like Broad > ChromHMM > > Dear Florian, > > I am trying to use your package Gviz to visualise my data and some data > from UCSC, for example: "Broad ChromHMM". But I have a error message. > I don't understand because I have checked with the package rtracklayer, > whose your package inherits, the name of tracks and tables. Could you help > me ? > > Regards > > Tiph > R Command used to find the name of track and table > >track.names["Broad ChromHMM"] > Broad ChromHMM > "wgEncodeBroadHmm" > > >sapply(track, function(track) { > + tableNames(ucscTableQuery(mySession, track=track)) > + }) > Broad ChromHMM > [1,] "wgEncodeBroadHmmGm12878HMM" > [2,] "wgEncodeBroadHmmH1hescHMM" > [3,] "wgEncodeBroadHmmK562HMM" > [4,] "wgEncodeBroadHmmHepg2HMM" > [5,] "wgEncodeBroadHmmHuvecHMM" > [6,] "wgEncodeBroadHmmHmecHMM" > [7,] "wgEncodeBroadHmmHsmmHMM" > [8,] "wgEncodeBroadHmmNhekHMM" > [9,] "wgEncodeBroadHmmNhlfHMM" > > UcscTrack(genome = gen, chrom > > My errors when I try to use UcscTrack: > > UcscTrack(genome = gen, chromosome = chr, track = "Broad ChromHMM", > + table="wgEncodeBroadHmmGm12878HMM", > + from = start, to = end, trackType = "AnnotationTrack", > + rstarts = "chromStart", rends = "chromEnd", gene = "name", > + symbol = "name", strand = "strand", > + fill = "itemRgb", name = "UCSC Genes") > > Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : > 'arg' should be one of "1000G Ph1 Accsbl", "1000G Ph1 Vars", "46-Way > Cons", "5% Lowest S", "acembly", "AceView Genes", "Affy Exon Array", "Affy > GNF1H", "Affy RNA Loc", "Affy U133", "Affy U133Plus2", "Affy U95", > "affyExonArray", "affyGnf1h", "affyU133", "affyU133Plus2", "affyU95", "All > SNPs(132)", "All SNPs(135)", "All SNPs(137)", "All SNPs(138)", "Allen > Brain", "allenBrainAli", "allHg19RS_BW", "altSeqComposite10", "Assembly", > "BAC End Pairs", "bacEndPairs", "Base Position", "BU ORChID", "Burge > RNA-seq", "burgeRnaSeqGemMapperAlign", "CCDS", "ccdsGene", "CD34 DnaseI", > "CGAP SAGE", "cgapSage", "chainSelf", "Chromosome Band", "clinvar", > "ClinVar Variants", "Common SNPs(132)", "Common SNPs(135)", "Common > SNPs(137)", "Common SNPs(138)", "Cons Indels MmCf", "cons100way", > "cons46way", "Conserv > > > > UcscTrack(genome = gen, chromosome = chr, track = "wgEncodeBroadHmm", > + table="wgEncodeBroadHmmGm12878HMM", > + from = start, to = end, trackType = "AnnotationTrack", > + rstarts = "chromStart", rends = "chromEnd", gene = "name", > + symbol = "name", strand = "strand", > + fill = "itemRgb", name = "UCSC Genes") > > Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : > 'arg' should be one of "1000G Ph1 Accsbl", "1000G Ph1 Vars", "46-Way > Cons", "5% Lowest S", "acembly", "AceView Genes", "Affy Exon Array", "Affy > GNF1H", "Affy RNA Loc", "Affy U133", "Affy U133Plus2", "Affy U95", > "affyExonArray", "affyGnf1h", "affyU133", "affyU133Plus2", "affyU95", "All > SNPs(132)", "All SNPs(135)", "All SNPs(137)", "All SNPs(138)", "Allen > Brain", "allenBrainAli", "allHg19RS_BW", "altSeqComposite10", "Assembly", > "BAC End Pairs", "bacEndPairs", "Base Position", "BU ORChID", "Burge > RNA-seq", "burgeRnaSeqGemMapperAlign", "CCDS", "ccdsGene", "CD34 DnaseI", > "CGAP SAGE", "cgapSage", "chainSelf", "Chromosome Band", "clinvar", > "ClinVar Variants", "Common SNPs(132)", "Common SNPs(135)", "Common > SNPs(137)", "Common SNPs(138)", "Cons Indels MmCf", "cons100way", > "cons46way", "Conserv > > > > -- > ---------------------------- > Tiphaine Martin > PhD Research Student | King's College > The Department of Twin Research & Genetic Epidemiology > Genetics & Molecular Medicine Division > St Thomas' Hospital > 4th Floor, Block D, > South Wing > SE1 7EH London > United Kingdom > > email : tiphaine.martin@kcl.ac.uk > Fax: +44 (0) 207 188 6761 > > [[alternative HTML version deleted]]
ADD REPLYlink written 4.3 years ago by Michael Lawrence10.0k
Ah, I see! Thanks for the clarification. That makes perfect sense. @Martin, I will provide a fix for the Gviz package in the next couple of days. Florian From: Michael Lawrence <lawrence.michael@gene.com<mailto:lawrence.michael@gene.com>> Date: Friday, February 21, 2014 2:23 PM To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Cc: Tiphaine Martin <tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk>>, "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>, Michael Lawrence <lawrence.michael@gene.com<mailto:lawrence.michael@gene.com>> Subject: Re: Gviz problem to extract some track with UcscTrack like Broad ChromHMM Hi Florian, trackNames,UCSCSession will only return the tracks in the actual browser. To get the track names from the table browser, just use trackNames,UCSCTableQuery. In other words, UCSCTableQuery is the interface to the table browser, while UCSCSession is the interface to the actual browser. Michael On Fri, Feb 21, 2014 at 1:40 AM, Hahne, Florian <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> wrote: Hi Martin, This seems to be a problem in the rtracklayer package: > library(rtracklayer) > session <- browserSession() > genome(session) <- "hg19" > grep("Broad", trackNames(session)) integer(0) > grep("Broad", names(trackNames(session))) integer(0) But: > query <- ucscTableQuery(session, "Broad ChromHMM") > tableNames(query) [1] "wgEncodeBroadHmmGm12878HMM" "wgEncodeBroadHmmH1hescHMM" [3] "wgEncodeBroadHmmK562HMM" "wgEncodeBroadHmmHepg2HMM" [5] "wgEncodeBroadHmmHuvecHMM" "wgEncodeBroadHmmHmecHMM" [7] "wgEncodeBroadHmmHsmmHMM" "wgEncodeBroadHmmNhekHMM" [9] "wgEncodeBroadHmmNhlfHMM" Even though the Broad ChromHMM track exists, it is not listed by trackNames(). The output of trackNames is used by Gviz to check whether the requested track exists in order to give a more useful error message. As a quick fix for now you could simply download the track data via rtracklayer into a GRanges object and use that as the input for your AnnotationTrack() constructor. Michael, is that a bug in rtracklayer, or is it intentional that trackNames does not list all available tracks? Broad ChromHMM is also listed in the table browser: http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=363821417&clade=mammal&o rg=Human&db=hg19&hgta_group=allTracks&hgta_track=wgEncodeBroadHmm&hgta _table=0&hgta_regionType=range&position=chr21%3A33%2C031%2C597-33%2C04 1%2C570&hgta_outputType=bed&hgta_outFileName= > sessionInfo() R version 3.0.2 Patched (2013-10-27 r64116) Platform: i386-apple-darwin12.5.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools parallel grid stats graphics grDevices utils [8] datasets methods base other attached packages: [1] rtracklayer_1.22.0 GenomicRanges_1.14.4 XVector_0.2.0 [4] IRanges_1.20.6 Biobase_2.22.0 BiocGenerics_0.8.0 [7] Gviz_1.6.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.24.0 biomaRt_2.18.0 Biostrings_2.30.1 [4] biovizBase_1.10.7 bitops_1.0-6 BSgenome_1.30.0 [7] cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 [10] dichromat_2.0-0 Formula_1.1-1 GenomicFeatures_1.14.2 [13] Hmisc_3.13-0 labeling_0.2 lattice_0.20-24 [16] latticeExtra_0.6-26 munsell_0.4.2 plyr_1.8 [19] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.14.2 [22] RSQLite_0.11.4 scales_0.2.3 splines_3.0.2 [25] stats4_3.0.2 stringr_0.6.2 survival_2.37-4 [28] XML_3.98-1.1 zlibbioc_1.8.0 Florian Hi, My genome is hg19 and I try to have the list of tables related to track "Broad ChromHMM ". I used the command line from rtracklayer to create the vector of potential tables. I put my sessionInfo(). Sorry to have forgotten to give you it. Also, I don't know if I am alone in this situation but when I read your documentation from web navigator (safari or firefox) or preview in mac OS X 10.6, I don't see the picture. Regards, Tiphaine On 17/02/14 08:31, Hahne, Florian wrote: Hi Martin, I'd really like to help, but from you code below I can't tell for which genome you are trying to do this (the value of 'gen'). I also have no idea how you came up with the 'track.name<http: track.name="">' vector. In general, Gviz is using rtracklayer::tableNames to figure out which tables and tracks are available. So you should get the same results, assuming that you checked for the same chromosome. Also please always include the output of sessionInfo() when asking for help in order for us to know which R and package version we are dealing with. Florian From: <martin>, Tiphaine <tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk>> Date: Thursday, February 13, 2014 11:18 PM To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Subject: Gviz problem to extract some track with UcscTrack like Broad ChromHMM Dear Florian, I am trying to use your package Gviz to visualise my data and some data from UCSC, for example: "Broad ChromHMM”. But I have a error message. I don’t understand because I have checked with the package rtracklayer, whose your package inherits, the name of tracks and tables. Could you help me ? Regards Tiph R Command used to find the name of track and table >track.names["Broad ChromHMM"] Broad ChromHMM “wgEncodeBroadHmm" >sapply(track, function(track) { + tableNames(ucscTableQuery(mySession, track=track)) + }) Broad ChromHMM [1,] "wgEncodeBroadHmmGm12878HMM" [2,] "wgEncodeBroadHmmH1hescHMM" [3,] "wgEncodeBroadHmmK562HMM" [4,] "wgEncodeBroadHmmHepg2HMM" [5,] "wgEncodeBroadHmmHuvecHMM" [6,] "wgEncodeBroadHmmHmecHMM" [7,] "wgEncodeBroadHmmHsmmHMM" [8,] "wgEncodeBroadHmmNhekHMM" [9,] "wgEncodeBroadHmmNhlfHMM" > UcscTrack(genome = gen, chrom My errors when I try to use UcscTrack: > UcscTrack(genome = gen, chromosome = chr, track = "Broad ChromHMM", + table="wgEncodeBroadHmmGm12878HMM", + from = start, to = end, trackType = "AnnotationTrack", + rstarts = "chromStart", rends = "chromEnd", gene = "name", + symbol = "name", strand = "strand", + fill = "itemRgb", name = "UCSC Genes”) Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : 'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv > UcscTrack(genome = gen, chromosome = chr, track = "wgEncodeBroadHmm", + table="wgEncodeBroadHmmGm12878HMM", + from = start, to = end, trackType = "AnnotationTrack", + rstarts = "chromStart", rends = "chromEnd", gene = "name", + symbol = "name", strand = "strand", + fill = "itemRgb", name = "UCSC Genes”) Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : 'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv -- ---------------------------- Tiphaine Martin PhD Research Student | King's College The Department of Twin Research & Genetic Epidemiology Genetics & Molecular Medicine Division St Thomas' Hospital 4th Floor, Block D, South Wing SE1 7EH London United Kingdom email : tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk> Fax: +44 (0) 207 188 6761<tel:%2b44%20%280%29%20207%20188%206761> [[alternative HTML version deleted]]
ADD REPLYlink written 4.3 years ago by florian.hahne@novartis.com1.6k
Hi, Thanks.In waiting, I did how you told me with rtracklayer ->GRanges object -> AnnotationTrack() contructor. I have a question about BiomartGeneRegionTrack. I would to visualize only at gene level, not at transcript level. But for each gene, I would like to see each exon and no only one long line with good color and maybe for the extrem 5'UTR, 3'UTR, the part of exon is thiner. I tried the different values of option "stacking" (squish,dense,hide) but none does what I would like and I tried also the option collapseTranscripts = TRUE; but it creates only one long bar. What I would like is like the combinaison of "collapseTranscripts = TRUE" (because It keep separatly the different gene) and "stacking="dense"" (because I can see the name of my gene and different exons). I hope that my explanation is enough understable. Do you know what I need to use for the options? I give you the different command lines that I did in R. Do I make a mistake with options to obtain that ? If it is the case, could you help me? Should I use BioMart + AnnotationTrack and other options to do that (I tried it but I don't succeed to do it)? > gen="hg19" > chr="2" > start=43625705 > end= 43826133 > biomTrack <- BiomartGeneRegionTrack(genome = gen, + chromosome = chr, start = start, + end = end, name = "ENSEMBL",stacking="squish") > biomTrack2 <- BiomartGeneRegionTrack(genome = gen, + chromosome = chr, start = start, + end = end, name = "ENSEMBL",stacking="dense") > biomTrack1 <- BiomartGeneRegionTrack(genome = gen, + chromosome = chr, start = start, + end = end, name = "ENSEMBL",stacking="hide") >martfunc <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >ensfunc <- getBM(c("ensembl_gene_id","ensembl_transcript_id","exon_chrom_start", + "exon_chrom_end","strand","gene_biotype","external_gene_id"), + filters = c("chromosome_name", "start", "end"), + values = list(chrEnsembl, start, end), mart=martfunc) >data_trackfunc <- AnnotationTrack(chr=chr,strand =ensfunc[,5],start=ensfunc[,3],end=ensfunc[,4], + feature=ensfunc[,6],group=ensfunc[,1],id=ensfunc[,7], + name = "genes ENSEMBL") > listtracks=c( biomTrack, biomTrack1, biomTrack2,data_trackfunc) > plotTracks(listtracks, from=start, to=end,showId=T) => create the plot "GViz_NOcollapseOption.png" >plotTracks(listtracks, from=start, to=end,showId=T,collapseTranscripts = TRUE, shape = "arrow", transcriptAnnotation = "symbol") => Create the plot "Gviz_collapseOption.png" > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.14.2 [3] AnnotationDbi_1.24.0 Biobase_2.22.0 [5] ggbio_1.10.11 ggplot2_0.9.3.1 [7] BiocInstaller_1.12.0 rtracklayer_1.22.3 [9] GenomicRanges_1.14.4 XVector_0.2.0 [11] IRanges_1.20.6 BiocGenerics_0.8.0 [13] Gviz_1.6.0 biomaRt_2.18.0 loaded via a namespace (and not attached): [1] Biostrings_2.30.1 biovizBase_1.10.7 bitops_1.0-6 [4] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 [7] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 [10] Formula_1.1-1 gridExtra_0.9.1 gtable_0.1.2 [13] Hmisc_3.14-0 labeling_0.2 lattice_0.20-24 [16] latticeExtra_0.6-26 MASS_7.3-29 munsell_0.4.2 [19] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 [22] RCurl_1.95-4.1 reshape2_1.2.2 Rsamtools_1.14.3 [25] RSQLite_0.11.4 scales_0.2.3 splines_3.0.2 [28] stats4_3.0.2 stringr_0.6.2 survival_2.37-7 [31] tools_3.0.2 VariantAnnotation_1.8.12 XML_3.95-0.2 [34] zlibbioc_1.8.0 Regards, Tiphaine On 21/02/14 13:29, Hahne, Florian wrote: > Ah, I see! Thanks for the clarification. That makes perfect sense. > @Martin, I will provide a fix for the Gviz package in the next couple > of days. > Florian > > From: Michael Lawrence <lawrence.michael at="" gene.com=""> <mailto:lawrence.michael at="" gene.com="">> > Date: Friday, February 21, 2014 2:23 PM > To: Florian Hahne <florian.hahne at="" novartis.com=""> <mailto:florian.hahne at="" novartis.com="">> > Cc: Tiphaine Martin <tiphaine.martin at="" kcl.ac.uk=""> <mailto:tiphaine.martin at="" kcl.ac.uk="">>, "bioconductor at r-project.org > <mailto:bioconductor at="" r-project.org="">" <bioconductor at="" r-project.org=""> <mailto:bioconductor at="" r-project.org="">>, Michael Lawrence > <lawrence.michael at="" gene.com="" <mailto:lawrence.michael="" at="" gene.com="">> > Subject: Re: Gviz problem to extract some track with UcscTrack like > Broad ChromHMM > > Hi Florian, > > trackNames,UCSCSession will only return the tracks in the actual > browser. To get the track names from the table browser, just use > trackNames,UCSCTableQuery. In other words, UCSCTableQuery is the > interface to the table browser, while UCSCSession is the interface to > the actual browser. > > Michael > > > On Fri, Feb 21, 2014 at 1:40 AM, Hahne, Florian > <florian.hahne at="" novartis.com="" <mailto:florian.hahne="" at="" novartis.com="">> wrote: > > Hi Martin, > This seems to be a problem in the rtracklayer package: > > > library(rtracklayer) > > session <- browserSession() > > genome(session) <- "hg19" > > > grep("Broad", trackNames(session)) > integer(0) > > > grep("Broad", names(trackNames(session))) > integer(0) > > But: > > query <- ucscTableQuery(session, "Broad ChromHMM") > > tableNames(query) > [1] "wgEncodeBroadHmmGm12878HMM" "wgEncodeBroadHmmH1hescHMM" > [3] "wgEncodeBroadHmmK562HMM" "wgEncodeBroadHmmHepg2HMM" > [5] "wgEncodeBroadHmmHuvecHMM" "wgEncodeBroadHmmHmecHMM" > [7] "wgEncodeBroadHmmHsmmHMM" "wgEncodeBroadHmmNhekHMM" > [9] "wgEncodeBroadHmmNhlfHMM" > > Even though the Broad ChromHMM track exists, it is not listed > by trackNames(). The output of trackNames is used by Gviz to check > whether the requested track exists in order to give a more useful > error message. As a quick fix for now you could simply download > the track data via rtracklayer into a GRanges object and use that > as the input for your AnnotationTrack() constructor. > > Michael, is that a bug in rtracklayer, or is it intentional that > trackNames does not list all available tracks? Broad ChromHMM is > also listed in the table browser: > http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=363821417&clade=ma mmal&org=Human&db=hg19&hgta_group=allTracks&hgta_track=wgEncodeBroadHm m&hgta_table=0&hgta_regionType=range&position=chr21%3A33%2C031%2C597-3 3%2C041%2C570&hgta_outputType=bed&hgta_outFileName= > > > sessionInfo() > R version 3.0.2 Patched (2013-10-27 r64116) > Platform: i386-apple-darwin12.5.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools parallel grid stats graphics grDevices utils > [8] datasets methods base > > other attached packages: > [1] rtracklayer_1.22.0 GenomicRanges_1.14.4 XVector_0.2.0 > [4] IRanges_1.20.6 Biobase_2.22.0 BiocGenerics_0.8.0 > [7] Gviz_1.6.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.24.0 biomaRt_2.18.0 Biostrings_2.30.1 > [4] biovizBase_1.10.7 bitops_1.0-6 BSgenome_1.30.0 > [7] cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 > [10] dichromat_2.0-0 Formula_1.1-1 GenomicFeatures_1.14.2 > [13] Hmisc_3.13-0 labeling_0.2 lattice_0.20-24 > [16] latticeExtra_0.6-26 munsell_0.4.2 plyr_1.8 > [19] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.14.2 > [22] RSQLite_0.11.4 scales_0.2.3 splines_3.0.2 > [25] stats4_3.0.2 stringr_0.6.2 survival_2.37-4 > [28] XML_3.98-1.1 zlibbioc_1.8.0 > > Florian > > > > > > Hi, > > My genome is hg19 and I try to have the list of tables related to > track "Broad ChromHMM ". I used the command line from rtracklayer > to create the vector of potential tables. > > I put my sessionInfo(). Sorry to have forgotten to give you it. > > Also, I don't know if I am alone in this situation but when I read > your documentation from web navigator (safari or firefox) or > preview in mac OS X 10.6, I don't see the picture. > > Regards, > Tiphaine > > On 17/02/14 08:31, Hahne, Florian wrote: >> Hi Martin, >> I'd really like to help, but from you code below I can't tell for >> which genome you are trying to do this (the value of 'gen'). I >> also have no idea how you came up with the 'track.name >> <http: track.name="">' vector. >> In general, Gviz is using rtracklayer::tableNames to figure out >> which tables and tracks are available. So you should get the same >> results, assuming that you checked for the same chromosome. >> Also please always include the output of sessionInfo() when >> asking for help in order for us to know which R and package >> version we are dealing with. >> Florian >> >> From: <martin>, Tiphaine <tiphaine.martin at="" kcl.ac.uk="">> <mailto:tiphaine.martin at="" kcl.ac.uk="">> >> Date: Thursday, February 13, 2014 11:18 PM >> To: Florian Hahne <florian.hahne at="" novartis.com="">> <mailto:florian.hahne at="" novartis.com="">> >> Subject: Gviz problem to extract some track with UcscTrack like >> Broad ChromHMM >> >> Dear Florian, >> >> I am trying to use your package Gviz to visualise my data and >> some data from UCSC, for example: "Broad ChromHMM?. But I have a >> error message. >> I don?t understand because I have checked with the >> package rtracklayer, whose your package inherits, the name of >> tracks and tables. Could you help me ? >> >> Regards >> >> Tiph >> R Command used to find the name of track and table >> >track.names["Broad ChromHMM"] >> Broad ChromHMM >> ?wgEncodeBroadHmm" >> >> >sapply(track, function(track) { >> + tableNames(ucscTableQuery(mySession, track=track)) >> + }) >> Broad ChromHMM >> [1,] "wgEncodeBroadHmmGm12878HMM" >> [2,] "wgEncodeBroadHmmH1hescHMM" >> [3,] "wgEncodeBroadHmmK562HMM" >> [4,] "wgEncodeBroadHmmHepg2HMM" >> [5,] "wgEncodeBroadHmmHuvecHMM" >> [6,] "wgEncodeBroadHmmHmecHMM" >> [7,] "wgEncodeBroadHmmHsmmHMM" >> [8,] "wgEncodeBroadHmmNhekHMM" >> [9,] "wgEncodeBroadHmmNhlfHMM" >> > UcscTrack(genome = gen, chrom >> >> My errors when I try to use UcscTrack: >> > UcscTrack(genome = gen, chromosome = chr, track = "Broad ChromHMM", >> + table="wgEncodeBroadHmmGm12878HMM", >> + from = start, to = end, trackType = "AnnotationTrack", >> + rstarts = "chromStart", rends = "chromEnd", gene = >> "name", >> + symbol = "name", strand = "strand", >> + fill = "itemRgb", name = "UCSC Genes?) >> >> Error in match.arg(track, sort(c(availTracks, >> names(availTracks)))) : >> 'arg' should be one of ?1000G Ph1 Accsbl?, ?1000G Ph1 Vars?, >> ?46-Way Cons?, ?5% Lowest S?, ?acembly?, ?AceView Genes?, ?Affy >> Exon Array?, ?Affy GNF1H?, ?Affy RNA Loc?, ?Affy U133?, ?Affy >> U133Plus2?, ?Affy U95?, ?affyExonArray?, ?affyGnf1h?, ?affyU133?, >> ?affyU133Plus2?, ?affyU95?, ?All SNPs(132)?, ?All SNPs(135)?, >> ?All SNPs(137)?, ?All SNPs(138)?, ?Allen Brain?, ?allenBrainAli?, >> ?allHg19RS_BW?, ?altSeqComposite10?, ?Assembly?, ?BAC End Pairs?, >> ?bacEndPairs?, ?Base Position?, ?BU ORChID?, ?Burge RNA-seq?, >> ?burgeRnaSeqGemMapperAlign?, ?CCDS?, ?ccdsGene?, ?CD34 DnaseI?, >> ?CGAP SAGE?, ?cgapSage?, ?chainSelf?, ?Chromosome Band?, >> ?clinvar?, ?ClinVar Variants?, ?Common SNPs(132)?, ?Common >> SNPs(135)?, ?Common SNPs(137)?, ?Common SNPs(138)?, ?Cons Indels >> MmCf?, ?cons100way?, ?cons46way?, ?Conserv >> >> >> > UcscTrack(genome = gen, chromosome = chr, track = "wgEncodeBroadHmm", >> + table="wgEncodeBroadHmmGm12878HMM", >> + from = start, to = end, trackType = "AnnotationTrack", >> + rstarts = "chromStart", rends = "chromEnd", gene = >> "name", >> + symbol = "name", strand = "strand", >> + fill = "itemRgb", name = "UCSC Genes?) >> >> Error in match.arg(track, sort(c(availTracks, >> names(availTracks)))) : >> 'arg' should be one of ?1000G Ph1 Accsbl?, ?1000G Ph1 Vars?, >> ?46-Way Cons?, ?5% Lowest S?, ?acembly?, ?AceView Genes?, ?Affy >> Exon Array?, ?Affy GNF1H?, ?Affy RNA Loc?, ?Affy U133?, ?Affy >> U133Plus2?, ?Affy U95?, ?affyExonArray?, ?affyGnf1h?, ?affyU133?, >> ?affyU133Plus2?, ?affyU95?, ?All SNPs(132)?, ?All SNPs(135)?, >> ?All SNPs(137)?, ?All SNPs(138)?, ?Allen Brain?, ?allenBrainAli?, >> ?allHg19RS_BW?, ?altSeqComposite10?, ?Assembly?, ?BAC End Pairs?, >> ?bacEndPairs?, ?Base Position?, ?BU ORChID?, ?Burge RNA-seq?, >> ?burgeRnaSeqGemMapperAlign?, ?CCDS?, ?ccdsGene?, ?CD34 DnaseI?, >> ?CGAP SAGE?, ?cgapSage?, ?chainSelf?, ?Chromosome Band?, >> ?clinvar?, ?ClinVar Variants?, ?Common SNPs(132)?, ?Common >> SNPs(135)?, ?Common SNPs(137)?, ?Common SNPs(138)?, ?Cons Indels >> MmCf?, ?cons100way?, ?cons46way?, ?Conserv > > > -- > ---------------------------- > Tiphaine Martin > PhD Research Student | King's College > The Department of Twin Research & Genetic Epidemiology > Genetics & Molecular Medicine Division > St Thomas' Hospital > 4th Floor, Block D, > South Wing > SE1 7EH London > United Kingdom > > email :tiphaine.martin at kcl.ac.uk <mailto:tiphaine.martin at="" kcl.ac.uk=""> > Fax:+44 (0) 207 188 6761 <tel:%2b44%20%280%29%20207%20188%206761> > > -- ---------------------------- Tiphaine Martin PhD Research Student | King's College The Department of Twin Research & Genetic Epidemiology Genetics & Molecular Medicine Division St Thomas' Hospital 4th Floor, Block D, South Wing SE1 7EH London United Kingdom email :tiphaine.martin at kcl.ac.uk Fax: +44 (0) 207 188 6761 -------------- next part -------------- A non-text attachment was scrubbed... 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ADD REPLYlink written 4.3 years ago by Tiphaine Martin40
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