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.