one.singlescan


	A numeric vector holding the phenotype value, or permuted phenotype value, for each individual. 


phenotype.vector


	A matrix of numeric phenotypes, which are to be associated with the phenotype.


genotype.mat


	A vector of 0's and 1's, indicating which markers are to be used as covariates in the model.
	

covar.vector


		An integer specifying the number of cores to be used in parallel processing.	

n.cores


This function is called by <code><a rd-options="" href="/link/pairscan.null?package=cape&version=2.0.2" data-mini-rdoc="cape::pairscan.null">pairscan.null</a></code> to generate a permuted list of marker effects. The top N markers are selected from this permutation, where N is the number of markers selected for the pairscan. These markers are then permuted in pairs to generate a null distribution for <code><a rd-options="" href="/link/pairscan?package=cape&version=2.0.2" data-mini-rdoc="cape::pairscan">pairscan</a></code>.


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

one.singlescan function


This function is called by <code><a rd-options='' href='pairscan.null'>pairscan.null</a></code> to generate a permuted list of marker effects. The top N markers are selected from this permutation, where N is the number of markers selected for the pairscan. These markers are then permuted in pairs to generate a null distribution for <code><a rd-options='' href='pairscan'>pairscan</a></code>.


one.singlescan: Runs one singlescan

Description

Usage

Arguments

Value

See Also