delete_underscore

Because cape uses underscores to separate marker names
from alleles, we need to delete any underscores that 
were present in the original marker names. This function
does that.

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

delete_underscore function

<dl><dt>data_obj</dt>
<dd>a <code>Cape</code> object</dd>
<dt>geno_obj</dt>
<dd>a genotype object</dd></dl>

Arguments

Delete underscores from marker names — delete_underscore

<dl>

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


<dt>geno_obj</dt>
<dd>a genotype object</dd>

</dl>

Delete underscores from marker names

delete_underscore: Delete underscores from marker names

Description

Usage

Value

Arguments