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

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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.

Author
Pedro Madrigal <pm12@sanger.ac.uk>, Pawel Krajewski <pkra@igr.poznan.pl>
Date of publication
None
Maintainer
Pedro Madrigal <pm12@sanger.ac.uk>
License
Artistic-2.0
Version
1.18.0

View on Bioconductor

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

Files in this package

NarrowPeaks/DESCRIPTION
NarrowPeaks/NAMESPACE
NarrowPeaks/R
NarrowPeaks/R/fpca.R
NarrowPeaks/R/getBindingProfiles.R
NarrowPeaks/R/getRandString.R
NarrowPeaks/R/list2matrix.R
NarrowPeaks/R/mergeSites.R
NarrowPeaks/R/narrowpeaks.R
NarrowPeaks/R/narrowpeaksDiff.R
NarrowPeaks/R/sitesCreator.R
NarrowPeaks/R/wig2CSARScore.R
NarrowPeaks/build
NarrowPeaks/build/vignette.rds
NarrowPeaks/data
NarrowPeaks/data/NarrowPeaks-dataset.rda
NarrowPeaks/inst
NarrowPeaks/inst/CITATION
NarrowPeaks/inst/NEWS
NarrowPeaks/inst/doc
NarrowPeaks/inst/doc/NarrowPeaks.R
NarrowPeaks/inst/doc/NarrowPeaks.Rnw
NarrowPeaks/inst/doc/NarrowPeaks.pdf
NarrowPeaks/man
NarrowPeaks/man/NarrowPeaks-internal.Rd
NarrowPeaks/man/NarrowPeaks-package.Rd
NarrowPeaks/man/narrowpeaks.Rd
NarrowPeaks/man/narrowpeaksDiff.Rd
NarrowPeaks/man/wig2CSARScore.Rd
NarrowPeaks/man/wigfile_test.Rd
NarrowPeaks/src
NarrowPeaks/src/wig2CSARScore.c
NarrowPeaks/src/wig2CSARScore_R_wrapper.c
NarrowPeaks/vignettes
NarrowPeaks/vignettes/NarrowPeaks.Rnw
NarrowPeaks/vignettes/NarrowPeaksVignette.bib