define_feature: Define the features on which reads will be counted

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Define the features on which reads will be counted

Description

Define the features on which reads will be counted

Usage

define_feature(ref = c("hg38","mm10", "ce11")[1],
 peak_file = NULL,
 bin_width  = NULL,
 genebody = FALSE,
 extendPromoter = 2500)

Arguments

ref	Reference genome
peak_file	A bed file if counting on peaks
bin_width	A number of bins if divinding genome into fixed width bins
genebody	A logical indicating if feature should be counted in genebodies and promoter.
extendPromoter	Extension length before TSS (2500).

Value

A GRanges object

Examples

gr_bins = define_feature("hg38", bin_width = 50000)
gr_genes = define_feature("hg38", genebody = TRUE, extendPromoter = 5000)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.