Define the features on which reads will be counted

Source: R/preprocessing_filtering_reduction.R

Define the features on which reads will be counted

define_feature(ref = c("hg38","mm10")[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)

#> ChromSCape::define_feature - Counting on genomic bins...
gr_genes = define_feature("hg38", genebody = TRUE, extendPromoter = 5000)