how to map choromosome location to gene ID
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Yan Jiao ▴ 140
@yan-jiao-4354
Last seen 7.1 years ago
Dear all, I'm trying to use biomaRt to map the chromosome location to gene ID,( I got chromosome number, start position and stop position, and it's for human) May I ask the syntax of it? Many thanks YAn [[alternative HTML version deleted]]
biomaRt biomaRt • 3.4k views
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@steffen-durinck-4465
Last seen 7.1 years ago
Hi Yan, This is a query similar to the one described in the biomaRt vignette section 4.5 http://bioconductor.org/packages/2.8/bioc/vignettes/biomaRt/inst/doc/b iomaRt.pdf for you that query might look like this: library(biomaRt) ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl") getBM(c("ensembl_gene_id","hgnc_symbol","start_position","end_position "), filters = c("chromosome_name", "start","end"), values = list(16, 1100000, 1250000), mart = ensembl) you'll get: ensembl_gene_id hgnc_symbol start_position end_position 1 ENSG00000162009 SSTR5 1122756 1131454 2 ENSG00000184471 C1QTNF8 1138226 1146244 3 ENSG00000196557 CACNA1H 1203241 1271771 4 ENSG00000181791 1115299 1116349 Cheers, Steffen On Wed, May 25, 2011 at 7:23 AM, Yan Jiao <y.jiao at="" ucl.ac.uk=""> wrote: > Dear all, > > I'm trying to use biomaRt to map the chromosome location to gene ID,( I got chromosome number, start position and stop position, and it's for human) > May I ask the syntax of it? > > Many thanks > > YAn > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >
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