js2264/aggregatr

aggregatR

The goal of aggregatR is to implement the AggregateCoverage S4 class in Bioconductor. This class standardizes the computation of average coverage of bigwig files across a number of genomic loci of same width and implements a plotting method to easily generate aggregate coverage plots for multiple bigwig files.

Installation

You can install the development version of aggregatR like so:

remotes::install_github('js2264/aggregatR')

aggregatR package is currently under submission to be integrated in Bioconductor. Once available there, the release version of this package can be installed like so:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install('aggregatR')

Example

library(GenomicRanges)
library(aggregatR)
library(ggplot2)
files <- data.frame(file = c(
    system.file('extdata', 'Scc1-calibrated_rep1.bw', package = 'aggregatR'),
    system.file('extdata', 'Scc1-calibrated_rep2.bw', package = 'aggregatR')
))
data(Scc1_peaks)
AC <- AggregatedCoverage(Scc1_peaks, files)
plot(AC) + 
    ggtitle('Average coverage of Scc1 ChIP-seq tracks over Scc1 peaks') + 
    labs(x = 'Distance to center of Scc1 peaks', y = 'Scc1 score', fill = 'file', col = 'file') +
    theme_bw()