MapAPAc: Map APAc with prebed to count region

In HHengUG/hatpal2: APA clusters calling and analysis

Description

Map APAc with prebed to count region

Usage

MapAPAc(
  RE_prebed,
  SA_prebed,
  APAc_file,
  out_dir,
  blocksize = 250,
  APAdist_cut = 25,
  SA_weight = 3
)

Arguments

RE_prebed	RE file of one strand generated from ExtractAPA()
SA_prebed	SA file of one strand generated from ExtractAPA()
APAc_file	APA clusters file from FilterAPAc()
out_dir	The directory where the output files are stored
blocksize	Threshold for isolated nodes and clusters (default 250)
APAdist_cut	Threshold for clustering the APA (default 25)
SA_weight	The weight increase of SA file (default 3)

Value

NULL, writes the output "APA_map.out" in the out_dir.

Examples

MapAPAc("rc_end.prebed", "sa.prebed", "APA_clusters.filtered.out", "output/")

HHengUG/hatpal2 documentation built on Dec. 17, 2021, 10:26 p.m.