README.md

In snystrom/rd4tools: An Interface to d4tools

rd4tools

rd4tools wraps the d4tools tool for reading & writing d4 files using R data structures.

Installation

Development Version

You can install the development version of rd4tools from GitHub with:

if (!requireNamespace("remotes", quietly=TRUE))
  install.packages("remotes")
remotes::install_github("snystrom/rd4tools")

library(rd4tools)

d4tools

rd4tools relies on a local install of d4tools. You can find binaries at the d4tools releases page, or if you have Rust installed, can compile from source using cargo install d4tools.

rd4tools provides d4_install_cargo() which will run cargo install d4tools from R, installing it in the users default cargo directory.

rd4tools needs to know the location of rd4tools on your local machine. If installing using cargo, rd4tools should autodetect the binary if installed at ~/.cargo/bin/d4tools. Otherwise, you can set the d4tools option once per session like so:

options("d4tools" = "path/to/d4tools")

Alternatively, all rd4tools functions contain the d4tools argument, which accepts a path to the d4tools binary.

To test whether R detects d4tools, run

d4_install_check()
#> checking main install
#> ✓ /home/rstudio/.cargo/bin

Examples

Examples are still a work-in-progress, but the following functions all work in my hands. See their man pages for details on usage.

• d4_create() convert a Bigwig, BAM, or CRAM file to d4 format.
• d4_view() returns signal within target regions as GRanges
• d4_view_genome() returns genome file used as Seqinfo
• d4_stat() returns summary statistics
• d4_histogram() returns a histogram of score values

Citation

Please cite the d4 authors if using rd4tools:

Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools. Hao Hou, Brent S Pedersen, Aaron Quinlan bioRxiv 2020.10.23.352567; doi: https://doi.org/10.1101/2020.10.23.352567

snystrom/rd4tools documentation built on Dec. 31, 2020, 7:29 a.m.