mvMAPIT: Multivariate Genome Wide Marginal Epistasis Test
Epistasis, commonly defined as the interaction between genetic
loci, is known to play an important role in the phenotypic variation of
complex traits. As a result, many statistical methods have been developed to
identify genetic variants that are involved in epistasis, and nearly all of
these approaches carry out this task by focusing on analyzing one trait at a
time. Previous studies have shown that jointly modeling multiple phenotypes
can often dramatically increase statistical power for association mapping. In
this package, we present the 'multivariate MArginal ePIstasis Test'
('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic
detection method which seeks to detect marginal epistasis or the combined
pairwise interaction effects between a given variant and all other variants.
By searching for marginal epistatic effects, one can identify genetic variants
that are involved in epistasis without the need to identify the exact
partners with which the variants interact – thus, potentially alleviating
much of the statistical and computational burden associated with conventional
explicit search based methods. Our proposed 'mvMAPIT' builds upon this
strategy by taking advantage of correlation structure between traits to
improve the identification of variants involved in epistasis.
We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a
multi-trait variance component estimation algorithm for efficient parameter
inference and P-value computation. Together with reasonable model
approximations, our proposed approach is scalable to moderately sized
genome-wide association studies.
Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>.
Stamp et al. (2023) <doi:10.1093/g3journal/jkad118>.
| Version: |
2.0.3 |
| Depends: |
R (≥ 3.5) |
| Imports: |
checkmate, CompQuadForm, dplyr, foreach, harmonicmeanp, logging, mvtnorm, Rcpp, stats, tidyr, utils |
| LinkingTo: |
Rcpp, RcppArmadillo, RcppParallel, RcppProgress, RcppSpdlog, testthat |
| Suggests: |
GGally, ggplot2, ggrepel, kableExtra, knitr, markdown, RcppAlgos, rmarkdown, testthat |
| Published: |
2023-09-26 |
| DOI: |
10.32614/CRAN.package.mvMAPIT |
| Author: |
Julian Stamp 
[cre, aut],
Lorin Crawford
[aut] |
| Maintainer: |
Julian Stamp <julian_stamp at brown.edu> |
| License: |
GPL (≥ 3) |
| URL: |
https://github.com/lcrawlab/mvMAPIT,
https://lcrawlab.github.io/mvMAPIT/ |
| NeedsCompilation: |
yes |
| Materials: |
README, NEWS |
| CRAN checks: |
mvMAPIT results |
Documentation:
Downloads:
Reverse dependencies:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=mvMAPIT
to link to this page.