[BioC] get promoter regions (bed format) of genes hg19
Ninni Nahm [guest]
guest at bioconductor.org
Wed Jan 22 10:12:35 CET 2014
I'm trying to obtain promoter regions of a list of genes.
This is my granges example:
htr_genes_gr = GRanges( seqnames = rep("chr1", 4),
ranges = IRanges(start = c(131025, 761586, 762988, 860260), end = c(134836, 794826, 794826, 879955)))
I wanted to use promoters(htr_genes_gr, upstream=2000)
to get the upstream regions. However, I get something, but Im afraid that it does not match with the USCS genome browser. So, I take the output and view it in IGV with hg19 loaded. But the promoter seems shifted, i.e. it does not start where the gene begins. When I look at the IRanges web page, there is an indication that the genome version might be hg18. I am not sure if this is the problem. Anyways, does anyone have a suggestion how I can get the bed file of the promoter regions. I need the promoter regions of all genes in the end.
Thanks a lot!
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
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