WaveSeqR-package: WaveSeq: A Wavelet-based Algorithm for Detecting Histone...

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

Description

WaveSeq is a highly sensitive peak-caller for detecting punctate and diffuse enrichment regions from ChIP-Seq data. WaveSeq utilizes the continuous wavelet transform framework. The algorithm involves the following steps:
(1) Pre-processing input data.
(2) Monte Carlo sampling to estimate wavelet coefficient thresholds.
(3) Use computed thresholds to call putative enrichment regions.
(4) Merging peaks within a user-specified distance
(5) Estimating FDR in the presence or absence of control data
(6) Correcting p-values for multiple testing.

Details

Package:	WaveSeqR
Type:	Package
Version:	1.0.2
Date:	2013-04-29
License:	GPL (>= 2)
LazyLoad:	yes

Author(s)

Apratim Mitra, Jiuzhou Song

Maintainer: Apratim Mitra <[e-mail]>, Jiuzhou Song <[e-mail]>

Examples

# load package
library(WaveSeqR)

# get paths to data files
WS.path <- system.file(package="WaveSeqR")
chip.file <- file.path(WS.path,"extdata","gabp_valouev2008_chr22-15m-30m-pad.graph")
control.file <- file.path(WS.path,"extdata","rxnoip_valouev2008_chr22-15m-30m-pad.graph")
test.dir <- file.path(WS.path,"extdata")

# ChIP-Seq analysis with control
waveseq(chip=chip.file,
	outdir=test.dir,
	control=control.file,
	exptname="GABP_valouev_chr22_control",
	preprocess=FALSE,
	thresdist=FALSE,
	gap=0,
	winsize=200,
	minreads=8,			
	adj.method="fdr")
	
# ChIP-Seq analysis without control
waveseq(chip=chip.file,
	outdir=test.dir,
	exptname="GABP_valouev_chr22_nocontrol",
	preprocess=FALSE,
	thresdist=FALSE,
	gap=0,
	winsize=200,
	minreads=8,
	samplesize=1e6,
	adj.method="fdr")

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