NarrowPeaks

This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see NarrowPeaks.

Functional Principal Component Analysis to Narrow Down Transcription Factor Binding Site Candidates

Bioconductor version: 2.10

The package processes data in wiggle track format (WIG) commonly produced by several ChIP-seq data analysis tools by applying functional version of principal component analysis (FPCA) over a set of selected candidate enriched regions. This is done in order to shorten the genomic locations accounting for a given proportion of variation among the enrichment-score profiles. It allows the user to discriminate between binding regions in close proximity to each other and to narrow 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.

Author: Pedro Madrigal <pm at engineering.com>, with contributions from Pawel Krajewski <pkra at igr.poznan.pl>

Maintainer: Pedro Madrigal <pm at engineering.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("NarrowPeaks")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NarrowPeaks")

Details

Package Archives

Follow Installation instructions to use this package in your R session.