ClusterAPA: Cluster the two-dimensional coordinate files (SA and RC/SA)...

In HHengUG/hatpal2: APA clusters calling and analysis

Description

Cluster the two-dimensional coordinate files (SA and RC/SA) to define the APA clusters

Usage

ClusterAPA(
  SA_prebed,
  uni_prebed,
  out_dir,
  gapdist_cut = 5,
  APAdist_cut = 25,
  RC_cutoff = 3,
  SA_weight = 3
)

Arguments

SA_prebed	SA file of one strand generated from ExtractAPA()
uni_prebed	rc_uni or SA file of one strand generated from ExtractAPA()
out_dir	The directory where the output files are stored
gapdist_cut	Threshold for filtering out isolated nodes (default 5)
APAdist_cut	Threshold for the gap between APA (default 25)
RC_cutoff	High observation nodes (default 3)
SA_weight	The weight of SA file (default 3)

Value

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

Examples

ClusterAPA("sa.prebed", "rc_uni.prebed", "output/")

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