pairscan_noKin

This internal function is called by <code>pairscan</code>
when no kinship correction is requested. It can be
compared to <code>pairscan_kin</code>. 
It fits pairwise linear models to estimate the effects of 
marker pairs on each trait.

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

pairscan_noKin function

<dl><dt>data_obj</dt>
<dd>a <code>Cape</code> object</dd>
<dt>pheno_mat</dt>
<dd>The matrix of trait values with individuals in rows
and traits in columns.</dd>
<dt>geno_mat</dt>
<dd>The matrix of genotypes to be tested</dd>
<dt>covar_table</dt>
<dd>The matrix of covariates with individuals in rows.</dd>
<dt>marker_pairs</dt>
<dd>A two-column matrix containing the marker pairs
to be tested.</dd>
<dt>n_perm</dt>
<dd>The number of permutations to be run</dd>
<dt>verbose</dt>
<dd>A logical value indicating whether to 
print progress to the screen</dd>
<dt>run_parallel</dt>
<dd>A logical value indicating 
whether parallel processing should be used</dd>
<dt>n_cores</dt>
<dd>The number of cores to be used if run_parallel is TRUE</dd></dl>

Arguments

Perform pairscan without a kinship correction — pairscan_noKin

<dl>

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


<dt>pheno_mat</dt>
<dd>The matrix of trait values with individuals in rows
and traits in columns.</dd>


<dt>geno_mat</dt>
<dd>The matrix of genotypes to be tested</dd>


<dt>covar_table</dt>
<dd>The matrix of covariates with individuals in rows.</dd>


<dt>marker_pairs</dt>
<dd>A two-column matrix containing the marker pairs
to be tested.</dd>


<dt>n_perm</dt>
<dd>The number of permutations to be run</dd>


<dt>verbose</dt>
<dd>A logical value indicating whether to 
print progress to the screen</dd>


<dt>run_parallel</dt>
<dd>A logical value indicating 
whether parallel processing should be used</dd>


<dt>n_cores</dt>
<dd>The number of cores to be used if run_parallel is TRUE</dd>

</dl>

Perform pairscan without a kinship correction

pairscan_noKin: Perform pairscan without a kinship correction

Description

Usage

Value

Arguments