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.

Package details

AuthorPedro Madrigal <[email protected]>, Pawel Krajewski <[email protected]>
Bioconductor views ChIPSeq Genetics Sequencing Transcription Visualization
MaintainerPedro Madrigal <[email protected]>
Package repositoryView on Bioconductor
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NarrowPeaks documentation built on May 31, 2017, 2:34 p.m.