bed2dyad: Convert a bed file to nucleosome dyad coverage

In musikutiv/tsTools: Toolbox for Functional Genomics Data Processing in R

Convert a bed file to nucleosome dyad coverage

Description

Single reads will be shifted towards the dyad position assuming an end-localisation of the read For paired reads the fragment mid points will be considered dyad position

Usage

bed2dyad(file.id, type = c("SINGLE", "PAIRED"), width = 1)

Arguments

file.id	path of the bed file
type	sequencing library type "SINGLE" or "PAIRED"
width	width of the dyad, default 1

Details

the bed files for SINGLE should have columns 1) chromosome 2) start 3) end 4) strand the bed files for PAIRED should have columns 1) chromosome 2) start 3) end

Value

a coverage object (RleList as returned by coverage)

musikutiv/tsTools documentation built on July 25, 2024, 2:42 a.m.