I am using ChIPseeker to annotate MACS2 peaks files from publicly available data. To begin, I'm trying to first annotate the peaks the way that the authors did in the publication.
This is what they say they did - "Gene annotation of the regions bound by indicated proteins were performed by GREAT version 3.0.0 (http://great.stanford.edu/public/html)... Association rule: Basal+extension: 5000 bp upstream, 1000 bp downstream, 1000000 bp max extension, curated regulatory domains included."
I don't plan to use GREAT. I am using ChIPseeker, the code for which is below. I've filled in what I can to recreate the annotation parameters they used, but am confused as to how I would incorporate "1000000 bp max extension, curated regulatory domains included" into the code.
##ChIPseeker Code
peak <- readPeakFile("Summits.bed")
peakAnno <- annotatePeak(peak, annoDb="org.Mm.eg.db", TxDb = txdb, tssRegion = c(-1000, 5000))
plotAnnoBar(peakAnno)
plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
write.csv(peakAnno, "Peak_annotated.csv")
Is there an easy way to incorporate "1000000 bp max extension, curated regulatory domains included" into ChIPseeker? Or are there other programs I can do to incorporate these parameters? Do these parameters really matter?
