Question: retrieving external Gene IDs from TranscriptDB Object
0
gravatar for Stefanie
6.4 years ago by
Stefanie360
Stefanie360 wrote:
Dear List, I have created a TranscriptDB for yeast as follows: library(GenomicFeatures) library(biomaRt) ## create yeast DB myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) myDBx <- cdsBy(myDB,by = "tx",use.names = TRUE) Now, I would like to retrieve the external gene ids. Is this the most generic way? # select mart and dataset mymart = useMart("ENSEMBL_MART_ENSEMBL", dataset = "scerevisiae_gene_ensembl", host="www.ensembl.org") # just a selection of transcripts sel = names(myDBx)[5:6] getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values = sel, filters = "ensembl_transcript_id", mart = mymart) And, when creating a TranscriptDB From UCSC: myDB1 <- makeTranscriptDbFromUCSC(genome = "hg19",tablename = "knownGene") myDBx1 <- cdsBy(myDB1,by = "tx",use.names =TRUE) What would be here the most generic way to retrieve the external gene IDs for each transcript ID? Best, Stefanie > sessionInfo() R Under development (unstable) (2013-05-02 r62711) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] biomaRt_2.16.0 GenomicFeatures_1.12.1 AnnotationDbi_1.22.3 [4] Biobase_2.20.0 GenomicRanges_1.12.2 IRanges_1.18.0 [7] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] Biostrings_2.28.0 bitops_1.0-5 BSgenome_1.28.0 DBI_0.2-6 [5] RCurl_1.95-4.1 Rsamtools_1.12.2 RSQLite_0.11.3 rtracklayer_1.20.1 [9] stats4_3.1.0 tools_3.1.0 XML_3.96-1.1 zlibbioc_1.6.0
yeast transcriptdb • 789 views
ADD COMMENTlink modified 6.4 years ago by Ugo Borello340 • written 6.4 years ago by Stefanie360
Answer: retrieving external Gene IDs from TranscriptDB Object
0
gravatar for Ugo Borello
6.4 years ago by
Ugo Borello340
France
Ugo Borello340 wrote:
Dear Stefanie, I just learned, thanks to Marc Carlson, an easy way to do what you want. It is nicely described in this vignette, section 05 (and 03): http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation Dbi/in st/doc/IntroToAnnotationPackages.pdf I hope this help. Ugo > From: Stefanie Tauber <stefanie.tauber at="" univie.ac.at=""> > Date: Mon, 6 May 2013 11:25:09 +0200 > To: <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] retrieving external Gene IDs from TranscriptDB Object > > Dear List, > > I have created a TranscriptDB for yeast as follows: > > library(GenomicFeatures) > library(biomaRt) > > ## create yeast DB > myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = > "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) > myDBx <- cdsBy(myDB,by = "tx",use.names = TRUE) > > Now, I would like to retrieve the external gene ids. > Is this the most generic way? > > # select mart and dataset > mymart = useMart("ENSEMBL_MART_ENSEMBL", dataset = > "scerevisiae_gene_ensembl", host="www.ensembl.org") > > # just a selection of transcripts > > sel = names(myDBx)[5:6] > > getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values = > sel, filters = "ensembl_transcript_id", mart = mymart) > > > And, when creating a TranscriptDB From UCSC: > > > myDB1 <- makeTranscriptDbFromUCSC(genome = "hg19",tablename = "knownGene") > myDBx1 <- cdsBy(myDB1,by = "tx",use.names =TRUE) > > What would be here the most generic way to retrieve the external gene IDs > for each transcript ID? > > Best, > Stefanie > > >> sessionInfo() > R Under development (unstable) (2013-05-02 r62711) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] biomaRt_2.16.0 GenomicFeatures_1.12.1 AnnotationDbi_1.22.3 > [4] Biobase_2.20.0 GenomicRanges_1.12.2 IRanges_1.18.0 > [7] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] Biostrings_2.28.0 bitops_1.0-5 BSgenome_1.28.0 DBI_0.2-6 > [5] RCurl_1.95-4.1 Rsamtools_1.12.2 RSQLite_0.11.3 > rtracklayer_1.20.1 > [9] stats4_3.1.0 tools_3.1.0 XML_3.96-1.1 zlibbioc_1.6.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 6.4 years ago by Ugo Borello340
Thanks for pointing out the vignette. Definitely helpful. Probably the way to go is downloading the corresponding org.*.db package and then use the appropriate keys. Thanks! Am 06.05.2013 um 12:18 schrieb Ugo Borello <ugo.borello@inserm.fr>: > Dear Stefanie, > I just learned, thanks to Marc Carlson, an easy way to do what you want. > It is nicely described in this vignette, section 05 (and 03): > http://www.bioconductor.org/packages/release/bioc/vignettes/Annotati onDbi/in > st/doc/IntroToAnnotationPackages.pdf > I hope this help. > Ugo > > >> From: Stefanie Tauber <stefanie.tauber@univie.ac.at> >> Date: Mon, 6 May 2013 11:25:09 +0200 >> To: <bioconductor@stat.math.ethz.ch> >> Subject: [BioC] retrieving external Gene IDs from TranscriptDB Object >> >> Dear List, >> >> I have created a TranscriptDB for yeast as follows: >> >> library(GenomicFeatures) >> library(biomaRt) >> >> ## create yeast DB >> myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = >> "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) >> myDBx <- cdsBy(myDB,by = "tx",use.names = TRUE) >> >> Now, I would like to retrieve the external gene ids. >> Is this the most generic way? >> >> # select mart and dataset >> mymart = useMart("ENSEMBL_MART_ENSEMBL", dataset = >> "scerevisiae_gene_ensembl", host="www.ensembl.org") >> >> # just a selection of transcripts >> >> sel = names(myDBx)[5:6] >> >> getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values = >> sel, filters = "ensembl_transcript_id", mart = mymart) >> >> >> And, when creating a TranscriptDB From UCSC: >> >> >> myDB1 <- makeTranscriptDbFromUCSC(genome = "hg19",tablename = "knownGene") >> myDBx1 <- cdsBy(myDB1,by = "tx",use.names =TRUE) >> >> What would be here the most generic way to retrieve the external gene IDs >> for each transcript ID? >> >> Best, >> Stefanie >> >> >>> sessionInfo() >> R Under development (unstable) (2013-05-02 r62711) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] biomaRt_2.16.0 GenomicFeatures_1.12.1 AnnotationDbi_1.22.3 >> [4] Biobase_2.20.0 GenomicRanges_1.12.2 IRanges_1.18.0 >> [7] BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] Biostrings_2.28.0 bitops_1.0-5 BSgenome_1.28.0 DBI_0.2-6 >> [5] RCurl_1.95-4.1 Rsamtools_1.12.2 RSQLite_0.11.3 >> rtracklayer_1.20.1 >> [9] stats4_3.1.0 tools_3.1.0 XML_3.96-1.1 zlibbioc_1.6.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > DI Stefanie Tauber Center for Integrative Bioinformatics Vienna (CIBIV) (CIBIV is a joint institute of Vienna University and Medical University) Max F. Perutz Laboratories (MFPL) Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 Dr. Bohr Gasse 9 A-1030 Wien, Austria Phone: ++43 +1 / 42772-4030 Fax: ++43 +1 / 42772-4098 email: stefanie.tauber@univie.ac.at www.cibiv.at [[alternative HTML version deleted]]
ADD REPLYlink written 6.4 years ago by Stefanie360
Yes, Look here at what Marc suggested me: http://article.gmane.org/gmane.science.biology.informatics.conductor/4 7912/m atch=borello Ugo From: Stefanie Tauber <stefanie.tauber@univie.ac.at> Date: Mon, 6 May 2013 13:05:31 +0200 To: Ugo Borello <ugo.borello@inserm.fr> Cc: <bioconductor@stat.math.ethz.ch> Subject: Re: [BioC] retrieving external Gene IDs from TranscriptDB Object Thanks for pointing out the vignette. Definitely helpful. Probably the way to go is downloading the corresponding org.*.db package and then use the appropriate keys. Thanks! Am 06.05.2013 um 12:18 schrieb Ugo Borello <ugo.borello@inserm.fr>: > Dear Stefanie, > I just learned, thanks to Marc Carlson, an easy way to do what you want. > It is nicely described in this vignette, section 05 (and 03): > http://www.bioconductor.org/packages/release/bioc/vignettes/Annotati onDbi/in > st/doc/IntroToAnnotationPackages.pdf > I hope this help. > Ugo > > >> From: Stefanie Tauber <stefanie.tauber@univie.ac.at> >> Date: Mon, 6 May 2013 11:25:09 +0200 >> To: <bioconductor@stat.math.ethz.ch> >> Subject: [BioC] retrieving external Gene IDs from TranscriptDB Object >> >> Dear List, >> >> I have created a TranscriptDB for yeast as follows: >> >> library(GenomicFeatures) >> library(biomaRt) >> >> ## create yeast DB >> myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = >> "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) >> myDBx <- cdsBy(myDB,by = "tx",use.names = TRUE) >> >> Now, I would like to retrieve the external gene ids. >> Is this the most generic way? >> >> # select mart and dataset >> mymart = useMart("ENSEMBL_MART_ENSEMBL", dataset = >> "scerevisiae_gene_ensembl", host="www.ensembl.org") >> >> # just a selection of transcripts >> >> sel = names(myDBx)[5:6] >> >> getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values = >> sel, filters = "ensembl_transcript_id", mart = mymart) >> >> >> And, when creating a TranscriptDB From UCSC: >> >> >> myDB1 <- makeTranscriptDbFromUCSC(genome = "hg19",tablename = "knownGene") >> myDBx1 <- cdsBy(myDB1,by = "tx",use.names =TRUE) >> >> What would be here the most generic way to retrieve the external gene IDs >> for each transcript ID? >> >> Best, >> Stefanie >> >> >>> sessionInfo() >> R Under development (unstable) (2013-05-02 r62711) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] biomaRt_2.16.0 GenomicFeatures_1.12.1 AnnotationDbi_1.22.3 >> [4] Biobase_2.20.0 GenomicRanges_1.12.2 IRanges_1.18.0 >> [7] BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] Biostrings_2.28.0 bitops_1.0-5 BSgenome_1.28.0 DBI_0.2-6 >> [5] RCurl_1.95-4.1 Rsamtools_1.12.2 RSQLite_0.11.3 >> rtracklayer_1.20.1 >> [9] stats4_3.1.0 tools_3.1.0 XML_3.96-1.1 zlibbioc_1.6.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > DI Stefanie Tauber Center for Integrative Bioinformatics Vienna (CIBIV) (CIBIV is a joint institute of Vienna University and Medical University) Max F. Perutz Laboratories (MFPL) Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 Dr. Bohr Gasse 9 A-1030 Wien, Austria Phone: ++43 +1 / 42772-4030 Fax: ++43 +1 / 42772-4098 email: stefanie.tauber@univie.ac.at www.cibiv.at <http: www.cibiv.at=""> [[alternative HTML version deleted]]
ADD REPLYlink written 6.4 years ago by Ugo Borello340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 197 users visited in the last hour