preprocess: Data preprocessing

In WaveSeqR: A Wavelet-based Method for ChIP-Seq peak calling

Description

Preprocesses an input bed file to generate summary bedgraph and padded bedgraph files for use with WaveSeqR. Also generates chromosome information file.

Usage

preprocess(infile, outdir, exptname, winsize = 200, fragsize = 150, redundancy = TRUE)

Arguments

infile	BED file to be preprocessed (required)
outdir	Output directory (required)
exptname	Unique string to identify name of experiment (required)
winsize	Window size for padded graph files (default=200)
fragsize	Library size used for sequencing (default=150)
redundancy	Logical value indicating whether redundant reads should be removed before calculating summary counts (default=TRUE)

Note

Function messages are piped to a log file which can be found in the log folder of outdir.

Author(s)

Apratim Mitra

WaveSeqR documentation built on May 2, 2019, 5:19 p.m.