ChIP to genes

Question

[roy.granit]

Hi All,

I have ChIP seq in the form of peaks per region:

chr start   end abs_summit  pileup  -log10(pvalue)  fold_enrichment -log10(qvalue)
chr1    856361  856664  856411  21  8.69656 4.06641 5.75518
chr1    859109  859948  859481  50  35.20025    9.42667 31.0408
chr1    877214  877610  877418  20  7.99405 3.88157 5.11687

I'm looking for some code or tool that can take these coordinates and map them onto genes.. e.g. find which genes (promoters) are bound by the investigated protein.

Thanks!

[ATpoint]

I typically do it manually using functions from GenomicRanges such as nearest(). Essentially you load your annotations into R, be it a GTF file from disk or annotations obtained with biomaRt, and then simply use nearest() to find the closest gene for each region. If you want to define a certain window so a maximum allowed distance between genes and regions you can use resize to first extend your regions by that window and then use subsetByOverlaps(). I do not think you need a specialized package beyond GenomicRanges here.

[GouthamAtla]

You can try this approach. A: Annotating narrow.peak to promoter region using GenomicFeatures

[roy.granit]

I found these tools: http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html and http://great.stanford.edu/public/html/