rd4tools wraps the d4tools tool for reading & writing d4 files using R data structures.
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)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/binExamples 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 asGRangesd4_view_genome()returns genome file used asSeqinfod4_stat()returns summary statisticsd4_histogram()returns a histogram of score values
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