splitsegs: splits segments that span chromosome ends

Description Usage Arguments

View source: R/segmenTools.R

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

1
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 Nov. 9, 2018, 5:38 p.m.