Select only peaks that are close to a gene promoter — gen_promoter

Select only peaks that are close to a gene promoter. In case of alternative promoters or multiple peaks close to the same promoter, the reads from all the peaks and promoters are summed.

Usage

gen_promoter_features(
  atac,
  upstream = 500,
  downstream = 50,
  tss_intervals = "intervs.global.tss",
  id_field = "geneSymbol"
)

Arguments

atac: a McPeaks or ScPeaks object
upstream: bp upstream to TSS
downstream: bp downstread from tss
tss_intervals: name of the intervals set with the TSS
id_field: the field in tss_intervals containing the gene names. Default: "geneSymbol"

Value

the McPeaks or ScPeaks object with new peaks which are a sum of the peaks within the defined promoters. The rownames of the atac@mat and the field 'peak_name' in atac@peaks would contain the name of the promoter (from id_field). Note that previous peak metadata and previous ignored peaks are dropped.

Examples

if (FALSE) {
atac_mc_promoters <- gen_promoter_features(atac_mc)
}