The Sparse Marginal Epistasis test

R-CMD-check.yaml CRAN downloads CRAN_Status_Badge

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.

Key Features

Installation

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

install.packages("devtools")
devtools::install_github("lcrawlab/sme")

Dependencies

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.

OpenMP

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

Known Issues

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.

References