cape: Combined Analysis of Pleiotropy and Epistasis for Diversity
Outbred Mice
Combined Analysis of Pleiotropy and Epistasis infers predictive
networks between genetic variants and phenotypes. It can be used with
standard two-parent populations as well as multi-parent populations, such
as the Diversity Outbred (DO) mice, Collaborative Cross (CC) mice, or the
multi-parent advanced generation intercross (MAGIC) population of Arabidopsis
thaliana. It uses complementary information of pleiotropic gene variants across
different phenotypes to resolve models of epistatic interactions between alleles.
To do this, cape reparametrizes main effect and interaction coefficients from
pairwise variant regressions into directed influence parameters. These
parameters describe how alleles influence each other, in terms of suppression
and enhancement, as well as how gene variants influence phenotypes. All of the
final interactions are reported as directed interactions between pairs of
parental alleles. For detailed descriptions of the methods used in this package
please see the following references.
Carter, G. W., Hays, M., Sherman, A. & Galitski, T. (2012) <doi:10.1371/journal.pgen.1003010>.
Tyler, A. L., Lu, W., Hendrick, J. J., Philip, V. M. & Carter, G. W. (2013) <doi:10.1371/journal.pcbi.1003270>.
| Version: |
3.1.1 |
| Depends: |
R (≥ 3.6) |
| Imports: |
abind, caTools, corpcor, doParallel, evd, foreach, here, igraph, Matrix, pheatmap, pracma, propagate, qtl, qtl2, qtl2convert, R6 (≥ 2.4.1), RColorBrewer (≥ 1.1-2), regress (≥ 1.3-21), shape (≥ 1.4.5), stats, tools, utils, yaml (≥
2.2.1) |
| Suggests: |
testthat (≥ 2.3.2), knitr (≥ 1.29), rmarkdown, parallel |
| Published: |
2022-05-19 |
| Author: |
Anna Tyler [aut, cre],
Jake Emerson [aut],
Baha El Kassaby [aut],
Ann Wells [aut],
Georgi Kolishovski [aut],
Vivek Philip [aut],
Gregory Carter [aut] |
| Maintainer: |
Anna Tyler <anna.tyler at jax.org> |
| License: |
GPL-3 |
| NeedsCompilation: |
no |
| Materials: |
README NEWS |
| CRAN checks: |
cape results |
Documentation:
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