MAPITR: MArginal ePIstasis Test for Regions

The MAPITR R package provides accessible functions for running the algorithms described in Turchin et al. 2020. MAPITR itself is a variance component model that tests for marginal epistasis -- the presence of any epistatic interactions -- between a given genetic pathway and the rest of the genome. MAPITR expects as input a set of genotypes, a single phenotype, and a list of pathways. As output, it returns for each pathway a p-value for the test against the null model of there not being any interactions between the pathway and the rest of the genome.

If you find a bug, or you have a question or feedback on our work, please post an issue.

Citing this work

If you find the MAPITR package or any of the source code in this repository useful for your work, please cite:

Turchin MC, Darnell G, Crawford L, and Ramachandran S (2020) "Pathway Analysis within Multiple Human Ancestries Reveals Novel Signals for Epistasis in Complex Traits".

License

Copyright (c) 2020, Michael Turchin, Gregory Darnell, Lorin Crawford, and Sohini Ramachandran.

All source code and software in this repository are made available under the terms of the MIT license. See file LICENSE for the full text of the license.

Quick Start

To install MAPITR from CRAN:

install.packages("MAPITR")

To install the most recent dev version of MAPITR from github:

install.packages("devtools")
devtools::install_github("mturchin20/MAPITR@v1.1.2", build_vignettes=TRUE)

Once you have installed the package, load the package in R:

library("MAPITR")

Next, view and run the example code provided in the introductory vignette using simulated data.

Credits

The MAPITR R package was developed by Michael Turchin at Brown University, with contributions from Peter Carbonetto, Greg Darnell, and Lorin Crawford.