footprintR: Tools for working with single-molecule footprinting data

Overview

footprintR provides tools for working with single-molecule footprinting data in R. These include functions for reading base modifications from bam files or files generated by modkit, efficient representation of such data as R objects, and functions to manipulate and visualize such objects.

Current contributors include:

• Panagiotis Papasaikas
• Sebastien Smallwood
• Charlotte Soneson
• Michael Stadler

Installation

footprintR can be installed from GitHub via the BiocManager package:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fmicompbio/footprintR")

Functionality

Here is a minimal example to for using footprintR:

library(footprintR)

infile <- system.file("extdata", "modkit_pileup_1.bed.gz", package = "footprintR")
se <- readBedMethyl(bmfile, modbase = "m")
se

assayNames(se)

The return value se is a SummarizedExperiment with positions in rows and samples in columns, and assays Nmod and Nvalid with the counts of modified and total (valid) bases.

The results can be conveniently visualized:

plotRegion(se)