get_eigentraits

a <code><a rd-options="" href="/link/Cape?package=cape&version=3.1.1" data-mini-rdoc="cape::Cape">Cape</a></code> object

data_obj

A logical value indicating whether to 
mean-center and standardize the traits.

scale_pheno

A logical value indicating whether to 
rankZ normalize the phenotypes.

normalize_pheno

This function uses singular value decomposition
(SVD) to calculate eigentraits from the phenotype 
matrix in the cape data object. It
adds the eigentrait matrix to the data object
along with the singular values and the right
singular vectors.

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>.

Anna L Tyler

cape

Combined Analysis of Pleiotropy and Epistasis for Diversity
Outbred Mice

Anna Tyler

Jake Emerson

Baha El Kassaby

Ann Wells

Georgi Kolishovski

Vivek Philip

Gregory Carter

get_eigentraits function

<dl><dt>data_obj</dt>
<dd>a <code>Cape</code> object</dd>
<dt>scale_pheno</dt>
<dd>A logical value indicating whether to 
mean-center and standardize the traits.</dd>
<dt>normalize_pheno</dt>
<dd>A logical value indicating whether to 
rankZ normalize the phenotypes.</dd></dl>

Arguments

Calculate eigentraits — get_eigentraits

<dl>

<dt>data_obj</dt>
<dd>a <code>Cape</code> object</dd>


<dt>scale_pheno</dt>
<dd>A logical value indicating whether to 
mean-center and standardize the traits.</dd>


<dt>normalize_pheno</dt>
<dd>A logical value indicating whether to 
rankZ normalize the phenotypes.</dd>

</dl>

get_eigentraits: Calculate eigentraits

Description

Usage

Value

Arguments

Details

Examples