pair_matrix

This function makes a matrix with two columns 
listing all pairwise combinations of the elements
of the input vector.

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

pair_matrix function

<dl><dt>elements</dt>
<dd>a vector containing elements from 
which to draw all possible pairs. Can be numeric or 
strings</dd>
<dt>ordered</dt>
<dd>A logical value indicating whether the order of the
pairs is important. If TRUE both a,b and b,a will be returned.
If FALSE, only a,b will be returned.</dd>
<dt>self_pairs</dt>
<dd>A logical value indicating whether self pairs
should be included. If TRUE, a,a will be returned. Otherwise it
will be excluded.</dd></dl>

Arguments

Get all pairs of elements in a vector — pair_matrix

<dl>

<dt>elements</dt>
<dd>a vector containing elements from 
which to draw all possible pairs. Can be numeric or 
strings</dd>


<dt>ordered</dt>
<dd>A logical value indicating whether the order of the
pairs is important. If TRUE both a,b and b,a will be returned.
If FALSE, only a,b will be returned.</dd>


<dt>self_pairs</dt>
<dd>A logical value indicating whether self pairs
should be included. If TRUE, a,a will be returned. Otherwise it
will be excluded.</dd>

</dl>

Get all pairs of elements in a vector

pair_matrix: Get all pairs of elements in a vector

Description

Usage

Value

Arguments