Dear All, I want to find the chromosome start and end positions in bp for a fragment delineated by two cytobands (eg. 5q13.1-5q13.2) ( in large scale). I tried getBM( ) in package 'biomaRt', but didn't find a right attribute to use. If using "chromosome_location", then I will get many locations instead of just 'start' and 'end' positions (see below). Should I extract the 1st and last positions from the resulted table, or any other ways to go using biomaRt, or even ways without using biomaRt? Many thanks! > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > res=getBM(attributes=c("chromosome_name","chromosome_location"),filter s=c("chromosome_name","band_start", "band_end"),values=list("5","q13.1", "q13.2"), mart=mart) > dim(res) [1] 12208 2 > res[1:10,] chromosome_name chromosome_location 1 5 NA 2 5 72892696 3 5 72893102 4 5 72893367 5 5 72893406 6 5 72893742 7 5 72893755 8 5 72893834 9 5 72893947 10 5 72894391 > sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.14.0 RCurl_0.9-3 loaded via a namespace (and not attached): [1] XML_1.95-3 > [[alternative HTML version deleted]]

On Thu, Oct 30, 2008 at 1:26 PM, Al Tango <time.is.flying at="" gmail.com=""> wrote: > Dear All, > > I want to find the chromosome start and end positions in bp for a fragment > delineated by two cytobands (eg. 5q13.1-5q13.2) ( in large scale). I tried > getBM( ) in package 'biomaRt', but didn't find a right attribute to use. If > using "chromosome_location", then I will get many locations instead of just > 'start' and 'end' positions (see below). Should I extract the 1st and last > positions from the resulted table, or any other ways to go using biomaRt, or > even ways without using biomaRt? > > Many thanks! > >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > res=getBM(attributes=c("chromosome_name","chromosome_location"),filt ers=c("chromosome_name","band_start", > "band_end"),values=list("5","q13.1", "q13.2"), mart=mart) > >> dim(res) > [1] 12208 2 >> res[1:10,] > chromosome_name chromosome_location > 1 5 NA > 2 5 72892696 > 3 5 72893102 > 4 5 72893367 > 5 5 72893406 > 6 5 72893742 > 7 5 72893755 > 8 5 72893834 > 9 5 72893947 > 10 5 72894391 Biomart is transcript/gene centric. This will get you gene chromosome locations between those two points, I think. Try this instead from UCSC, instead: t <- tempfile() download.file('http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database /cytoBand.txt.gz',t) cytobands <- read.table(gzfile(t),sep="\t") cytobands[1:5,] V1 V2 V3 V4 V5 1 chr1 0 2300000 p36.33 gneg 2 chr1 2300000 5300000 p36.32 gpos25 3 chr1 5300000 7100000 p36.31 gneg 4 chr1 7100000 9200000 p36.23 gpos25 5 chr1 9200000 12600000 p36.22 gneg Sean >> sessionInfo() > R version 2.7.1 (2008-06-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_1.14.0 RCurl_0.9-3 > > loaded via a namespace (and not attached): > [1] XML_1.95-3 >> > > [[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 >