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