knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
The goal of megadepth
is to provide an R interface to the command line tool Megadepth for BigWig and BAM related utilities created by Christopher Wilks. This R package enables fast processing of BigWig files on downstream packages such as dasper and recount3. The Megadepth software also provides utilities for processing BAM files and extracting coverage information from them.
Here is an illustration on how fast megadepth
is compared to other tools for processing local and remote BigWig files.
Throughout the documentation we use a capital M
to refer to the software by Christopher Wilks and a lower case m
to refer to this R/Bioconductor package.
Get the latest stable R
release from CRAN. Then install megadepth
using from Bioconductor the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("megadepth")
And the development version from GitHub with:
BiocManager::install("LieberInstitute/megadepth")
In the following example, we install Megadepth with install_megadepth()
, which downloads a binary for your OS (Linux, Windows or macOS). We can then use with an example BigWig file to compute the coverage at a set of regions.
## Load the R package library("megadepth") ## Install Megadepth's pre-compiled binary on your system install_megadepth() ## Next, we locate the example BigWig and annotation files example_bw <- system.file("tests", "test.bam.all.bw", package = "megadepth", mustWork = TRUE ) annotation_file <- system.file("tests", "testbw2.bed", package = "megadepth", mustWork = TRUE ) ## We can then use megadepth to compute the coverage bw_cov <- get_coverage(example_bw, op = "mean", annotation = annotation_file) bw_cov
Megadepth is very powerful and can do a lot of different things. The R/Bioconductor package provides two functions for interfacing with Megadepth, megadepth_cmd()
and megadepth_shell()
. For the first one, megadepth_cmd()
, you need to know the actual command syntax you want to use and format it accordingly. If you are more comfortable with R functions, megadepth_shell()
uses r BiocStyle::CRANpkg("cmdfun")
to power this interface and capture the standard output stream into R.
To make it easier to use, megadepth
includes functions that simplify the number of arguments, read in the output files, and converts them into R/Bioconductor friendly objects, such as get_coverage()
illustrated above.
We hope that you'll find megadepth
and Megadepth useful for your work. If you are interested in checking how fast megadepth
is, check out the speed analysis comparison against other tools. Note that the size of the files used and the number of genomic regions queried will affect the speed comparisons.
## R-like interface ## that captures the standard output into R head(megadepth_shell(help = TRUE)) ## Command-like interface megadepth_cmd("--help")
x <- megadepth_shell(help = TRUE) cat(paste0(x, "\n"))
Below is the citation output from using citation('megadepth')
in R. Please
run this yourself to check for any updates on how to cite megadepth.
print(citation("megadepth"), bibtex = TRUE)
Please note that the megadepth
was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
Please note that the megadepth
project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
r BiocStyle::CRANpkg('usethis')
, r BiocStyle::CRANpkg('remotes')
, r BiocStyle::Githubpkg('r-hub/sysreqs')
and r BiocStyle::CRANpkg('rcmdcheck')
customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck')
.r BiocStyle::CRANpkg('covr')
.r BiocStyle::CRANpkg('pkgdown')
.r BiocStyle::CRANpkg('styler')
.r BiocStyle::CRANpkg('devtools')
and r BiocStyle::CRANpkg('roxygen2')
.For more details, check the dev
directory.
This package was developed using r BiocStyle::Biocpkg('biocthis')
.
ReCount
projectThe main documentation website for all the recount3
-related projects is available at recount.bio. Please check that website for more information about how this R/Bioconductor package and other tools are related to each other.
r BiocStyle::Biocpkg('megadepth')
was made possible to David Zhang, the author of r BiocStyle::Biocpkg("dasper")
, and a member of the Mina Ryten's lab at UCL.
The ReCount
family involves the following teams:
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