Summary and scope

wigglescout is an R library that allows you to calculate summary values across bigWig files and BED files and visualize them in a genomics-relevant manner. It is based on broadly used libraries such as rtracklayer and GenomicRanges, among others for calculation, and mostly ggplot2 for visualization. You can look at the DESCRIPTION file to get more information about all the libraries that make this one possible.

There are also many other tools whose functionality overlaps a little or much with wigglescout, but there was no single tool that included all that I needed. The aim of this library is therefore not to replace any of those tools, or to provide a silver-bullet solution to genomics data analysis, but to provide a comprehensive, yet simple enough set of tools focused on bigWig files that can be used entirely from the R environment without switching back and forth across tools.

Other tools and libraries for akin purposes that you may be looking for include: deepTools, SeqPlots, bwtool, wiggletools, and the list is endless!

wigglescout allows you to summarize and visualize the contents of bigWig files in two main ways:

• Genome-wide. Genome is partitioned on equally-sized bins and their aggregated value is calculated. Useful to get a general idea of the signal distribution without looking at specific places.
• Across sets of loci. This can be either summarized categories, or individual values, as in genome-wide analyses.

wigglescout functionality is built in two layers. Names of functions that calculate values over bigWig files start with bw_. These return GRanges objects when possible, data.frame objects otherwise (i.e. when values are summarized over some category, genomic location is lost in this process).

On the other hand, functions that plot such values and that usually make internal use of bw_ functions, start with plot_.

Installation

wigglescout is a package under development. You will need remotes to install it (and devtools if you plan to work on it):

install.packages(c('devtools', 'remotes'))

Additionally, there was an issue in the past with installing dependencies that come from BioConductor repository. This seems to have been fixed now, but if you run into problems, I recommend installing manually these dependencies before running the installation:

install.packages(('BiocManager'))
BiocManager::install(c('GenomeInfoDb', 'GenomicRanges', 'rtracklayer'))

Then you can install directly from this GitHub repository:

library(remotes)
install_github('cnluzon/wigglescout', build_vignettes=TRUE)

Getting started

The vignettes as they can give a comprehensive overview of what is available in the package. You can check the vignettes with browseVignettes("wigglescout").

These are the groups of functions that are included in wigglescout:

• bwtools. Functionality to handle bigWig files. Importing, binning and intersecting, aggregating BED files. This relies heavily on rtracklayer calculations.

• bwplot. Make plots out of bwtools calculations.

Troubleshooting

Q: When running install_github I get the following error:

Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded
Execution halted

A: This seemed to be a problem that came from installing Bioconductor dependencies. A workaround is installing the BioConductor packages manually:

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

BiocManager::install(c('GenomeInfoDb', 'GenomicRanges', 'rtracklayer'))