compareWithControl: Compare ChIP to Control

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

Description

Part of the controlFDR function. This function reads in a list of putative peaks, fetches reads in those regions from the control data and compares the two using a two-sided exact Binomial test. Both sets of reads are normalized to per million mapped reads before performing the test.

Usage

compareWithControl(peaks, chip, control, winsize = 200, minreads = 8, binom.sided = "two.sided")

Arguments

peaks	File containing peak locations. Must be in bedGraph format.
chip	Padded bedGraph file for the ChIP data being analyzed.
control	Padded bedGraph file for the control data being analyzed.
winsize	Window size used for obtaining peaks(default = 200 bp).
minreads	Minimum reads in a peak (default = 8). This filtering is necessary for a more accurate estimation of false discovery rate.
binom.sided	One-sided or two-sided binomial test, if control is not NA (default = "two.sided")

Details

For a detailed description of the bedGraph file format see http://genome.ucsc.edu/goldenPath/help/bedgraph.html.

Value

Returns a matrix containing peak locations, fold changes and their corresponding p-values sorted by chromosome. Has the following columns:

chromosome	Chromosome name
start	Start position of peak (1-based indexing)
end	End position of peak
ChIP.reads	Number of ChIP reads in the peak (normalized to per million mapped reads)
Control.reads	Number of control reads in the peak (normalized to per million mapped reads)
Fold.change	Fold change calculated as chip/control
p-value	P-value for the peak obtained from two-sided exact binomial test binom.test

Warning

For small window sizes for the padded bedGraph files and consequently large file sizes, reading the data may take a long time.

Author(s)

Apratim Mitra

See Also

binom.test, getPeakReads

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