The smer package implements a computationally and
statistically efficient method for detecting marginal epistasis in
genome-wide association studies (GWAS). Find the full package
documentation including examples and articles here: Sparse Marginal Epistasis test
Documentation.
You can install the latest release from CRAN
install.packages("smer")You can install the development version of smer from GitHub with:
install.packages("devtools")
devtools::install_github("lcrawlab/sme")System requirements of the package:
To install Rhdf5lib, first install the tool
BiocManager from CRAN, then install the library using this
tool.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rhdf5lib")The full list of R dependencies can be found in the DESCRIPTION file.
For OS X and Linux, the OpenMP library can be installed via one of the (shell) commands specified below:
| System | Command |
|---|---|
| OS X (using Homebrew) | brew install libomp |
| Debian-based systems (including Ubuntu) | sudo apt-get install libomp-dev |
To enable openMP, it may be necessary to configure the compiler flags
SHLIB_OPENMP_CXXFLAGS and LDFLAGS in the
~/.R/Makevars file.
| System | Required Flags |
|---|---|
| OS X | -Xclang -fopenmp -lomp |
| Linux | -fopenmp -lomp |
If the error is ld: library "crypto" not found, install
openssl (e.g. brew install openssl).
Compiling the package requires the compiler to find the libraries for
the dependencies. For unix systems, the libraries are typically
installed at /usr/local/lib and
/usr/local/include. For users using OS X and homebrew, the
libraries are typically installed at /opt/homebrew/lib and
/opt/homebrew/include.
Non-standard library paths need to be configured. The
src/Makevars file configures the compiler flags and
considers the LDFLAGS and CPPFLAGS from the
~/.R/Makevars file.