NarrowPeaks (version 1.16.0)
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Description
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.