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

Description Usage Arguments Value

View source: R/reporting.r

Description

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

Usage

1
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.