splitsegs: splits segments that span chromosome ends

In raim/segmenTools: Tools for Functional Genome Exploration

splits segments that span chromosome ends

Description

Finds segments that span chromosomes ends and splits those in two segments on each covered chromosome. The input must contain columns "start" and "end"; these will be modified for chromosome-spanning segments. All other entries in the matrix will be copied, unless an "idcol" is specified, which will receive the suffix "_2" for one of two copies.

Usage

splitsegs(segs, chrS, idcol, verb = 0)

Arguments

segs	a matrix of segment start and end coordinates given in columns named "start" and "end"
chrS	a chromosome index, indicating at wich positions chromosomes start; this is required for handling chromosome ends and forward and reverse strand values
idcol	column holding segment IDs; IDs of split segments will receive the suffix "_2" for once copy#'
verb	integer level of verbosity, 0: no messages, 1: show messages

raim/segmenTools documentation built on March 20, 2024, 6:23 a.m.