getPeakReads: Get Reads Within a List of Specified Locations

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

Description

Part of the compareWithControl function. Extracts reads falling within specified locations from a data frame obtained from a padded bedGraph file.

Usage

getPeakReads(peak.mat, reads.mat, winsize = 200)

Arguments

peak.mat	Data frame containing peak locations. Has four columns: chromosome, start, end, reads
reads.mat	Data frame containing read counts from a padded bedGraph file. Has the same columns as peak.mat.
winsize	Window size used for obtaining peaks(default = 200 bp).

Value

A vector of same length as the number of rows of peak.mat containing read counts extracted from read.mat.

Warning

read.mat must be obtained from a padded bedGraph file as output by the WaveSeq preprocessing pipeline.

Author(s)

Apratim Mitra

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