maTracks: Write BED and BIGWIG files for normalized, filter-passed...

In jeffbhasin/methylaction: MethylAction: Differentially Methylated Regions (DMRs) from MBD-isolated Genome Sequencing (MiGS/MBD-seq)

Description

Creates a BED file suitable for uploading as a custom track to the UCSC genome browser.

Usage

maTracks(ma, reads, path = ".", bigwig = FALSE, ncore = 1)

Arguments

ma	Output list from a run of methylaction()
reads	Preprocessed reads/fragments data from getReads()
path	Folder to save the files in, will create if does not exist
bigwig	If TRUE, convert the BED to BIGWIG files, requires wigToBigWig in $PATH (obtain from the Jim Kent source tree)
ncore	Number of parallel processes to use

Value

Writes BED file to disk and optionally converts to a bigWig file.

jeffbhasin/methylaction documentation built on May 17, 2017, 3:59 p.m.