Hi,

I am relatively new to R and analysing ChIPseq data sets and have a query.

I have used MACS2 callpeak for IP and input samples to find significantly enriched peaks for 2 proteins. I have the resulting summits.bed and .narrowPeak files. I can use these with e.g. ChIPseeker getPromoters and getTagMatrix to produce a heatmap or profile following the instructions to show TSS regions and read count frequency.

My question is how can i use the enriched peaks from one dataset as the windows for another set ? e.g. to see if a protein has a number of reads mapped within 3000 bases upstream or downstream of the peak centre from another protein.

Thanks

Rob

Generally speaking, you can read the bed files into R using rtracklayer, which will create a GRanges object. You could then use resize to make the GRanges object to increase the width of the peaks for the first protein, and then use findOverlaps to see what (expanded) peaks from protein 1 overlap the unexpanded peaks of protein 2.

You should read the vignettes for GenomicFeatures and rtracklayer for more background.