NarrowPeaks: Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Version 1.20.0

The package applies a functional version of principal component analysis (FPCA) to: (1) Postprocess data in wiggle track format, commonly produced by generic ChIP-seq peak callers, by applying FPCA over a set of read-enriched regions (ChIP-seq peaks). This is done to study variability of the the peaks, or to shorten their genomic locations accounting for a given proportion of variation among the enrichment-score profiles. (2) Analyse differential variation between multiple ChIP-seq samples with replicates. The function 'narrowpeaksDiff' quantifies differences between the shapes, and uses Hotelling's T2 tests on the functional principal component scores to identify significant differences across conditions. An application of the package for Arabidopsis datasets is described in Mateos, Madrigal, et al. (2015) Genome Biology: 16:31.

AuthorPedro Madrigal <pm12@sanger.ac.uk>, Pawel Krajewski <pkra@igr.poznan.pl>
Bioconductor views ChIPSeq Genetics Sequencing Transcription Visualization
Date of publicationNone
MaintainerPedro Madrigal <pm12@sanger.ac.uk>
LicenseArtistic-2.0
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("NarrowPeaks")

Getting started

Package overview

Popular man pages

narrowpeaks: Detect Narrow Peaks from Enrichment-Score Profiles
narrowpeaksDiff: Differential Analysis of Transcription Factor Binding using...
NarrowPeaks-internal: NarrowPeaks internal functions
NarrowPeaks-package: Shape-based Analysis of Variation in ChIP-seq using...
wig2CSARScore: Convert Data from a Wiggle Track (WIG) File to CSAR Binary...
wigfile_test: Example Wiggle Track Produced After ChIP-seq Data Analysis
See all...

All man pages Function index File listing

Man pages

narrowpeaks: Detect Narrow Peaks from Enrichment-Score Profiles
narrowpeaksDiff: Differential Analysis of Transcription Factor Binding using...
NarrowPeaks-internal: NarrowPeaks internal functions
NarrowPeaks-package: Shape-based Analysis of Variation in ChIP-seq using...
wig2CSARScore: Convert Data from a Wiggle Track (WIG) File to CSAR Binary...
wigfile_test: Example Wiggle Track Produced After ChIP-seq Data Analysis

Functions

NarrowPeaks Man page
NarrowPeaks-dataset Man page
NarrowPeaks-package Man page
fpca Man page Source code
getBindingProfiles Man page Source code
getRandString Man page Source code
list2matrix Man page Source code
mergeSites Man page Source code
narrowpeaks Man page Source code
narrowpeaksDiff Man page Source code
sitesCreator Man page Source code
wig2CSARScore Man page Source code
wigfile_test Man page

Files

DESCRIPTION
NAMESPACE
R
R/fpca.R
R/getBindingProfiles.R
R/getRandString.R
R/list2matrix.R
R/mergeSites.R
R/narrowpeaks.R
R/narrowpeaksDiff.R
R/sitesCreator.R
R/wig2CSARScore.R
build
build/vignette.rds
data
data/NarrowPeaks-dataset.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/NarrowPeaks.R
inst/doc/NarrowPeaks.Rnw
inst/doc/NarrowPeaks.pdf
man
man/NarrowPeaks-internal.Rd
man/NarrowPeaks-package.Rd
man/narrowpeaks.Rd
man/narrowpeaksDiff.Rd
man/wig2CSARScore.Rd
man/wigfile_test.Rd
src
src/wig2CSARScore.c
src/wig2CSARScore_R_wrapper.c
vignettes
vignettes/NarrowPeaks.Rnw
vignettes/NarrowPeaksVignette.bib
NarrowPeaks documentation built on May 20, 2017, 10:19 p.m.