hictkR

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R bindings for hictk, a blazing fast toolkit to work with .hic and .cool files.

If you are looking for the Python API, checkout the hictkpy repository.

Installing hictkR

hictkR can be installed from CRAN or from GitHub using devtools:

# Install from CRAN
install.packages("hictkR")

# Install from GitHub
install.packages("devtools")
devtools::install_github("paulsengroup/hictkR@v0.1.0")

hictkR contains extensions written in C++ that need to be compiled before hictkR itself is installed.

This requires a compiler toolchain supporting C++17, such as:

• GCC 8+
• Clang 8+
• Apple-Clang 10.0+

On Windows a suitable compiler toolchain can be installed using Rtools.

More details about the build process

hictkR depends on the libhictk, the C++ library that underlies hictk.

libhictk is a header-only library that depends on several third-party packages, such as boost and HDF5.

Instead of requiring users to manually install all the required dependencies, hictkR comes with a configure (and configure.win) script that download, configure, and build the required dependencies using Conan.

In brief, here is what the script does:

• Setup a temporary folder inside the package build folder.
  All temporary files are created inside this folder, which is automatically deleted after hictkR has been successfully installed
• Generate a cleanup script to remove build artifacts when calling e.g. devtools::install(args=c("--clean"))
• Download uv from astral.sh
• Use uv to create an environment with conan, cmake, and ninja.
  If a modern version of Python is not available on the host machine, then uv will first download and install Python inside the temporary folder.
  Python is required to run Conan
• Configure Conan such that all build artifacts are stored inside the package temporary folder
• Run script tools/generate_makevars.py to do the following:
  • Use Conan to build hictk and all of its dependencies (see tools/conanfile.py)
    Special care has been taken to ensure that only necessary dependencies are built.
    For example, while hictk depends on boost, it only requires a handful of its components (most of which are header-only).
    Thus, Conan is instructed to only build boost modules that are strictly needed
  • Generate a Makevars file with the appropriate include paths and link flags, such that the R build system can find hictk and all of its dependencies

Once the Makevars has been generated, it is placed inside src/, and the rest of the build process is driven by R’s build system.

On Windows, there’s an additional step to build b2, which is required to build boost.
Conan is supposed to install, and if necessary, build b2, but this does not work in the Rtools build environment.

You can customize where temporary files are placed using the following two environment variables:

• HICTKR_TMPDIR: this is where all temporary files generated by the configure script are stored
• HICTKR_CONAN_HOME: this is used to set the CONAN_HOME variable, where all build files generate by Conan are stored.
  If you are debugging build failures, it may be a good idea to set this variable, such that Conan does not have to build all of the dependency from scratch every time

Finally, Conan is configured to preferentially use the C and C++ compilers set through the CC and CXX environment variables.
Thus, on Linux and macOS, we recommend setting these variables to the same compiler used by R.

Using hictkR

library(hictkR)

path <- "file.mcool"  # "file.hic"
f <- File(path, resolution=100000)

df <- fetch(f, "chr1:0-10,000,000", "chr2:0-20,000,000", join=TRUE)
df

chrom1	start1	end1	chrom2	start2	end2	count
chr1	0	100000	chr2	0	100000	15
chr1	0	100000	chr2	100000	200000	5
chr1	0	100000	chr2	300000	400000	17
chr1	0	100000	chr2	400000	500000	22
chr1	0	100000	chr2	500000	600000	30
chr1	0	100000	chr2	600000	700000	21
chr1	0	100000	chr2	600000	700000	21
…	…	…	…	…	…	…

Refer to the manual and vignette available at paulsengroup.github.io/hictkR for more examples on how to use hictkR.

Citing

If you use hictkR in you research, please cite the following publication:

Roberto Rossini, Jonas Paulsen, hictk: blazing fast toolkit to work with .hic and .cool files Bioinformatics, Volume 40, Issue 7, July 2024, btae408, https://doi.org/10.1093/bioinformatics/btae408

BibTex

@article{hictk,
    author = {Rossini, Roberto and Paulsen, Jonas},
    title = "{hictk: blazing fast toolkit to work with .hic and .cool files}",
    journal = {Bioinformatics},
    volume = {40},
    number = {7},
    pages = {btae408},
    year = {2024},
    month = {06},
    issn = {1367-4811},
    doi = {10.1093/bioinformatics/btae408},
    url = {https://doi.org/10.1093/bioinformatics/btae408},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/40/7/btae408/58385157/btae408.pdf},
}