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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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.