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:	3.1.2
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:	2024-01-09
DOI:	10.32614/CRAN.package.cape
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:

Reference manual:	cape.pdf
Vignettes:	cape: A package for the combined analysis of pleiotropy and epistasis

Downloads:

Package source:	cape_3.1.2.tar.gz
Windows binaries:	r-devel: cape_3.1.2.zip, r-release: cape_3.1.2.zip, r-oldrel: cape_3.1.2.zip
macOS binaries:	r-release (arm64): cape_3.1.2.tgz, r-oldrel (arm64): cape_3.1.2.tgz, r-release (x86_64): cape_3.1.2.tgz, r-oldrel (x86_64): cape_3.1.2.tgz
Old sources:	cape archive

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