make_anno_dt: make_anno_dt

In FrietzeLabUVM/ssvQC: QC for enrichment based NGS

make_anno_dt

Description

make_anno_dt

Usage

make_anno_dt(peak_grs, anno_grs, name_lev = NULL)

Arguments

peak_grs	a named list of GRanges where each feature set should be annotated. Use output from easyLoad_narrowPeak or similar.
anno_grs	a named list of GRanges where each corresponds to an annotated feature type. Use output from make_anno_grs
name_lev	Optional levels to impose order in feature sets. Default of NULL uses input order of peak_grs.

Value

data.table with annotation overlaps for inerval sets in peak_grs.

Examples

gtf_file = system.file(package = "seqqc", "extdata/gencode.v35.annotation.at_peaks.gtf")
anno_grs = make_anno_grs(gtf_file)

peak_files = dir(system.file("extdata", package = "seqqc"),
  pattern = "Peak$", full.names = TRUE)
peak_grs = seqsetvis::easyLoad_narrowPeak(peak_files)

make_anno_dt(peak_grs, anno_grs)

FrietzeLabUVM/ssvQC documentation built on Jan. 20, 2025, 8:19 a.m.