source("http://bioconductor.org/biocLite.R")
biocLite("NarrowPeaks")

NarrowPeaks

Analysis of Variation in ChIP-seq using Functional PCA Statistics

Bioconductor version: 2.13

The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process data in wiggle track format (WIG) commonly produced by ChIP-seq peak finders by applying FPCA over a set of selected candidate enriched regions. This is done in order to shorten the genomic locations accounting for a given proportion of variation among the enrichment-score profiles. The function 'narrowpeaks' allows the user to discriminate between binding regions in close proximity to each other and to narrow down the length of the putative transcription factor binding sites while preserving the information present in the variability of the dataset and capturing major sources of variation. (2) Analyze differential variation when multiple ChIP-seq samples need to compared. The function 'narrowpeaksDiff' quantifies differences between the tag-enrichment, and uses non-parametric tests on the FPC scores for testing differences between conditions.

Author: Pedro Madrigal <pm at engineering.com>, with contributions from Pawel Krajewski <pkra at igr.poznan.pl>

Maintainer: Pedro Madrigal <pm at engineering.com>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("NarrowPeaks")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NarrowPeaks")

 

PDF	R Script	NarrowPeaks Vignette I. Intra-sample variability: Splitting and narrowing down ChIP-seq peaks in a single experiment.
PDF	R Script	NarrowPeaks Vignette II. Inter-sample variability: Analysis of variation in differential binding across ChIP-seq samples.
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPseq, Genetics, Software, Transcription, Visualization
Version	1.6.0
In Bioconductor since	BioC 2.10 (R-2.15)
License	Artistic-2.0
Depends	R (>= 2.10.0), splines
Imports	GenomicRanges, IRanges, fda, CSAR
Suggests	rtracklayer, GenomicRanges, CSAR
System Requirements
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Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	NarrowPeaks_1.6.0.tar.gz
Windows Binary	NarrowPeaks_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	NarrowPeaks_1.6.0.tgz
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