biomaRt query: retrieve exon locations etc
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.1 years ago
Hi All, Sorry for the naive question! I was trying to retrieve some coordinates (start and end positions) from biomaRt and I'm not sure if I'm doing things right… Problem definition: For a gene, retrieve the 5'UTR and exon coordinates for the most common isoform of the gene. *************** library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") getAtt <- c('chromosome_name', 'start_position', 'end_position', 'strand','exon_chrom_start','exon_chrom_end',         '5_utr_start','5_utr_end','3_utr_start','3_utr_end') elocs <- getBM(attributes=getAtt,filters="hgnc_symbol",value="ZMYM4",m art=ensembl) print(elocs) ************** However, this would give me the coordinates for all isoforms and it would be difficult to get the coordinates for the most common isoform. How can I identify the most common isoform? many thanks! [[alternative HTML version deleted]]
biomaRt biomaRt • 2.6k views
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@steffen-durinck-4465
Last seen 7.1 years ago
Hi Tim, There is no filter for getting the cannonical transcript only. Something that gets close is filtering for transcripts that have a ccds id, adding this to your query only returns one transcript: elocs <- getBM(attributes=c(getAtt,"ensembl_transcript_id"),filters=c("hgnc_sym bol","with_ccds"),value=list("ZMYM4",TRUE),mart=ensembl) Cheers, Steffen On Fri, Jan 25, 2013 at 12:46 PM, Tim Smith <tim_smith_666@yahoo.com> wrote: > Hi All, > > Sorry for the naive question! I was trying to retrieve some coordinates > (start and end positions) from biomaRt and I'm not sure if I'm doing things > right > > Problem definition: For a gene, retrieve the 5'UTR and exon coordinates > for the most common isoform of the gene. > > *************** > library(biomaRt) > ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") > > getAtt <- c('chromosome_name', 'start_position', 'end_position', > 'strand','exon_chrom_start','exon_chrom_end', > '5_utr_start','5_utr_end','3_utr_start','3_utr_end') > > elocs <- > getBM(attributes=getAtt,filters="hgnc_symbol",value="ZMYM4",mart=ens embl) > print(elocs) > > ************** > > However, this would give me the coordinates for all isoforms and it would > be difficult to get the coordinates for the most common isoform. How can I > identify the most common isoform? > > many thanks! > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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