[BioC] get promoter regions (bed format) of genes hg19

Ninni Nahm [guest] guest at bioconductor.org
Wed Jan 22 10:12:35 CET 2014

Dear all,

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)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list