get_geno_with_covar

For pairwise testing, cape appends the covariates
to the genotype matrix. This function performs
that task.

internal

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_geno_with_covar function

<dl><dt>data_obj</dt>
<dd>The cape object. See <code>Cape</code>.</dd>
<dt>geno_obj</dt>
<dd>A genotype object.</dd>
<dt>g_covar</dt>
<dd>A logical value indicating whether to append
genotype-derived covariates to the final matrix. Defaults to TRUE.</dd>
<dt>p_covar</dt>
<dd>A logical value indicating whether to append
phenotype-derived covariates to the final matrix. Defaults to TRUE.</dd>
<dt>for_pairscan</dt>
<dd>If TRUE, the function returns the genotype matrix 
already designated for the pairscan. Otherwise it returns the full
genotype matrix as specified by data_obj$geno_names.</dd></dl>

Arguments

Return the genotype matrix with covariates 
added. — get_geno_with_covar

<dl>

<dt>data_obj</dt>
<dd>The cape object. See <code>Cape</code>.</dd>


<dt>geno_obj</dt>
<dd>A genotype object.</dd>


<dt>g_covar</dt>
<dd>A logical value indicating whether to append
genotype-derived covariates to the final matrix. Defaults to TRUE.</dd>


<dt>p_covar</dt>
<dd>A logical value indicating whether to append
phenotype-derived covariates to the final matrix. Defaults to TRUE.</dd>


<dt>for_pairscan</dt>
<dd>If TRUE, the function returns the genotype matrix 
already designated for the pairscan. Otherwise it returns the full
genotype matrix as specified by data_obj$geno_names.</dd>

</dl>

Return the genotype matrix with covariates 
added.

get_geno_with_covar: Return the genotype matrix with covariates added.

Description

Usage

Value

Arguments