rd4

Overview

The Dense Depth Data Dump (D4) format provides fast analysis and compact storage of quantitative genomics datasets. rd4 provides R bindings for reading and querying D4 files. For full details on the format, see Hou et al. (https://doi.org/10.1038/s43588-021-00085-0).

Installation

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

BiocManager::install("rd4")

Usage

library(rd4)
browseVignettes("rd4")

For developers

R dependencies

Consider using renv to isolate an R environment for rd4 development.

• remotes
• rextendr
• devtools
• BiocCheck

Developing an R package using Rust code

Note: these steps have already been done for rd4 and don't need to be repeated by new developers.

• rextendr package
• Instructions on setting up and developing a package

Build and test the package locally

Build Rust code

cd src/rust/
cargo build

Build and check R package within an R session

# Set working directory to package root
setwd(".")

# Compile Rust code into R functions and auto-generate R documentation (yes, rextendr::document() does both)
rextendr::document()

# Load the package
devtools::load_all()

# Run tests
devtools::test()

# Run CRAN and/or Bioconductor checks
devtools::check()
BiocCheck::BiocCheck()

Add new Rust code

rextendr vignette

Test Rust code

cd src/rust/
cargo test

Formatting of auto-generated R code

Auto-generated R code produced by rextendr may not satisfy formatting requirements for Bioconductor or CRAN. Consider using an automatic formatter like formatr to auto-format before submission, or the Code -> Reformat Code workflow in Rstudio.