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

[Valerie Obenchain]

Hi Ninni,

A more complete description of the promoters() function is on the man 
page in the GenomicRanges package. You can find this by specifying the 
full method name:

   ?'promoters,GenomicRanges-method'

The GRanges or GRangesList you supply as 'x' is assumed to contain gene 
ranges. Here is a snip from the man page stating that the assumption is 
that start(x) is the TSS:

>         • ‘promoters’ returns an object of the same type and length as
>           ‘x’ containing promoter ranges. Promoter ranges extend around
>           the transcription start site (TSS) which is defined as
>           ‘start(x)’. The ‘upsteam’ and ‘downstream’ arguments define
>           the number of nucleotides in the 5' and 3' direction,
>           respectively. The full range is defined as,
>
>           (start(x) - upstream) to (start(x) + downstream - 1).

So promoters() simply returns the region upstream and/or downstream of 
the range you supply as 'x'. If you have a generic range and want to 
determine if it falls within a gene you can use findOverlaps() on a 
TranscriptDb and your ranges.

   library(TxDb.Hsapiens.UCSC.hg19.knownGene)
   txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
   genes <- transcriptsBy(txdb, "gene")
   hits <- findOverlaps(htr_genes_gr, genes)

'queryHits' is an index of 'htr_genes_gr' ranges that maps to the 
'subjectHits' index of 'genes' ranges. Here we see that both range 2 and 
4 in 'htr_genes_gr' each map to 2 different genes.

>> hits
> Hits of length 6
> queryLength: 4
> subjectLength: 23459
>   queryHits subjectHits
>    <integer>   <integer>
>  1         1       19185
>  2         2       17448
>  3         2       20105
>  4         3       17448
>  5         4        5026
>  6         4        8270

Isolate the genes that the ranges in 'htr_genes_gr' hit:

   mygenes <- genes[subjectHits(hits)]

Call promoters() on the gene ranges of interest.

   promoters(mygenes, upstream=2000)


Valerie

On 01/22/2014 01:12 AM, Ninni Nahm [guest] wrote:
>
> 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():
>
>   sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
Valerie Obenchain

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: vobencha at fhcrc.org
Phone:  (206) 667-3158
Fax:    (206) 667-1319