get.geno.with.covar


	The object in which all results are stored. See <code><a rd-options="" href="/link/read.population?package=cape&version=2.0.2" data-mini-rdoc="cape::read.population">read.population</a></code>.
	

data.obj


	The object in which genotype data are stored. See <code><a rd-options="" href="/link/read.geno?package=cape&version=2.0.2" data-mini-rdoc="cape::read.geno">read.geno</a></code>.
	

geno.obj


	A logical value indicating whether covariates derived from genetic markers should be included.
	

g.covar


	A logical value indicating whether covariates derived from phenotypes should be included.
	

p.covar


	A logical value indicating if the full genotype matrix should be returned, or only the markers being evaluated in the pairscan.
	

for.pairscan


This function is similar to get.geno, but it returns the genotype matrix with covariates appended for greater ease of testing all marker pairs including covariates. Covariates derived from genetic markers are placed in the appropriate location based on chromosome coordinates.


internal

Combines complementary information across multiple related
phenotypes to infer directed epistatic interactions between genetic markers.
This analysis can be applied to a variety of engineered and natural populations.

Anna L Tyler

cape

Combined Analysis of Pleiotropy and Epistasis

get.geno.with.covar function


	The object in which all results are stored. See <code><a rd-options='' href='read.population'>read.population</a></code>.
	


	The object in which genotype data are stored. See <code><a rd-options='' href='read.geno'>read.geno</a></code>.
	

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get.geno.with.covar: Retrieve the genotype matrix with the covariates appended.

Description

Usage

Arguments

Value

See Also