select_eigentraits

This function is used to identify which eigentraits
will be analyzed in the Cape run. After eigentrait 
decomposition of n traits, there will be n eigentraits.
If there are more than two eigentraits, the user may
wish to analyze a subset of them. This function specifies
which of the eigentraits will be analyzed by Cape. It does
this by subsetting the ET matrix to only those eigentraits
specified. The traits not selected are deleted from the object.

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

select_eigentraits function

<dl><dt>data_obj</dt>
<dd>a <code>Cape</code> object</dd>
<dt>traits_which</dt>
<dd>A vector of integers, of at least length two
specifying which eigentraits should be analyzed.</dd></dl>

Arguments

Assign selected eigentraits in the Cape object — select_eigentraits

<dl>

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


<dt>traits_which</dt>
<dd>A vector of integers, of at least length two
specifying which eigentraits should be analyzed.</dd>

</dl>

select_eigentraits: Assign selected eigentraits in the Cape object

Description

Usage

Value

Arguments

See Also

Examples