Package: NarrowPeaks
Version: 1.8.0
Date: 2014-03-14
Type: Package
Title: Analysis of Variation in ChIP-seq using Functional PCA
Author: Pedro Madrigal <pm59@cam.ac.uk>, with contributions from
        Pawel Krajewski <pkra@igr.poznan.pl>
Description: The package applies a functional
        version of principal component analysis (FPCA) to: (1) Process
        data in wiggle track format (WIG) commonly produced by ChIP-seq
        peak callers by applying FPCA over a set of read-enriched
    	regions (ChIP-seq peaks). 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 splitting and trimming binding sites in
        close proximity to each other, narrowing 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) Analyse
        differential variation between multiple ChIP-seq samples with 
	replicates. The function 'bigwigdiff' quantifies differences
        between the shapes, and uses Hotelling's T2 tests on
        the functional principal component scores to identify 
	significant differences between conditions.
Depends: R (>= 2.10.0), splines
Maintainer: Pedro Madrigal <pmb59@cam.ac.uk>
Imports: GenomicRanges, IRanges, fda, CSAR
Suggests: rtracklayer, GenomicRanges, CSAR, BiocStyle
License: Artistic-2.0
biocViews: Visualization, ChIPSeq, Transcription, Genetics, Sequencing,
        Sequencing
Packaged: 2014-04-12 09:51:54 UTC; biocbuild
Built: R 3.1.0; i386-w64-mingw32; 2014-04-12 15:17:12 UTC; windows
Archs: i386, x64
