annotate_peaks: Annotation of peaks

In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Description

This function categorises peaks as either promoter, genebody or intergenic based on the distance from a known transcription start site (TSS) and gene overlap. By default, the distance is set to 1500 bp but can be changed with the 'tssdist' argument. The function also allows regions that are within a certain distance of each other to be merged to form a larger region. The merge distance is set as default to 0 (i.e. they have to be touching) but may be changed with the 'mergedist' argument, and will only merge peaks within the same region (i.e. distal peaks will not be merged with proximal peaks).

Usage

annotate_peaks(regions, merge = TRUE, mergedist = 0, tssdist = 1500,
  species = c("human", "mouse"))

Arguments

regions	GRanges object of peaks to annotate
merge	Boolean indicating whether to merge peaks or not
mergedist	Maximum distance apart for peaks to be merged
tssdist	Distance from TSS to classify as a proximal or distal peak
species	character string specifying the name of the species. Only 'human', and 'mouse' are supported at present. [DEFAULT = human].

Value

GRanges object of annotated peaks

anilchalisey/chompR documentation built on May 9, 2019, 3:59 a.m.