controlFDR: FDR Estimation with Control

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

Description

Estimates FDR for peaks in a ChIP sample by comparing it with a control data set. controlFDR consists of three steps:
(1) Compare ChIP reads with control reads within peaks using compareWithControl().
(2) Adjust p-values for multiple testing using p.adjust.
(3) Print peaks and p-values to file.

Usage

controlFDR(peaks, chip, control, outfile, winsize = 200,
			minreads = 8, binom.sided = "two.sided", adj.method = "fdr")

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.
outfile	Output file.
winsize	Window size for obtaining peaks (default = 200).
minreads	Minimum reads within a peak (default = 8). This filtering is necessary for a more accurate estimation of FDR.
binom.sided	One-sided or two-sided binomial test, if control is not NA (default = "two.sided")
adj.method	Method for multiple testing adjustment. Can use any methods accepted by p.adjust (default = "fdr").

Value

This function writes peaks to a file after FDR estimation in the presence of control. This file has with the following fields:

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.reads/Control.reads
p.value	P-value for the peak
adj.p.value	P-values adjusted for multiple comparisons using adj.method

Author(s)

Apratim mitra

See Also

p.adjust, binom.test

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