Hi I have a liste of reads that map to the genome in certain position (chromosome | position) and i would like to know which function allows that. Thanks in advance for your help, Regards, Ramzi [[alternative HTML version deleted]]

Hi, using Biomart you can get the gene name, ensembl_id, entrezgene id, using your chromosome positions as filters. check the pdf of biomart, there you can find good examples, that explain just how to do that. Good luck, Andreia On Tue, Nov 24, 2009 at 12:18 PM, Ramzi TEMANNI <ramzi.temanni@gmail.com>wrote: > Hi > I have a liste of reads that map to the genome in certain position > (chromosome | position) and i would like to know which function allows > that. > Thanks in advance for your help, > Regards, > Ramzi > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Andreia Fonseca <andreia.fonseca at="" gmail.com=""> writes: > Hi, > > using Biomart you can get the gene name, ensembl_id, entrezgene id, using > your chromosome positions as filters. check the pdf of biomart, there you > can find good examples, that explain just how to do that. IRanges::findOverlaps can help do this for many reads. To do so, represent the biomaRt data as a RangedData object library(IRanges) library(biomaRt) mart <- useMart('ensembl', 'mmusculus_gene_ensembl') attr <- c("chromosome_name", "start_position", "end_position", "ensembl_gene_id") bm <- getBM(attr, "chromosome_name", as.character(1:19), mart) rd <- with(bm, RangedData(IRanges(start_position, end_position), space=chromosome_name, ensembl_gene_id)) and also your reads. (If the reads come from ShortRead, then reads <- as(ShortRead::readAligned(<...>), "RangesList") but it will be more memory efficient to input just the read chromosome, start, and aligned width). Then olap <- findOverlaps(reads, rd) and associate the results (e.g., number of hits per gene) with the biomaRt information for down-stream calculations with rd[["hits"]] <- tabulate(subjectHits(olap), nrow(rd)) Martin > Good luck, > Andreia > > On Tue, Nov 24, 2009 at 12:18 PM, Ramzi TEMANNI <ramzi.temanni at="" gmail.com="">wrote: > >> Hi >> I have a liste of reads that map to the genome in certain position >> (chromosome | position) and i would like to know which function allows >> that. >> Thanks in advance for your help, >> Regards, >> Ramzi >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793