scanonevar: scanonevar

In rcorty/vqtl: Genome Scans to Accommodate and Target Genetic and Non-Genetic Effects on Trait Variance in Test Crosses

Description

scanonevar conducts a genome scan in an experimental cross, accommodating covariate effects in residual variance and identifying genetic effects on residual variance.

Usage

scanonevar(cross, mean.formula = phenotype ~ mean.QTL.add + mean.QTL.dom,
  var.formula = ~var.QTL.add + var.QTL.dom, chrs = qtl::chrnames(cross
  = cross), scan_types = c("mQTL", "vQTL", "mvQTL"),
  glm_family = "gaussian", return.covar.effects = FALSE)

Arguments

cross	The cross, built by qtl to be used in mapping
mean.formula	The formula to describe the mean of the phenotype. Keywords are mean.QTL.add and mean.QTL.dom for the additive and dominance components of the QTL effect on the mean. dglm model will be fit if mean.formula has only fixed effects. hglm model will be fit if mean.formula has one or more random effects.
var.formula	The formula to describe the residual variance of the phenotype. Keywords are var.QTL.add and var.QTL.dom for the additive and dominance components of the QTL effect on residual phenotype variance. var.formula must have only fixed effects.
chrs	chromosomes to scan
scan_types	a vector containing at least one of 'mQTL', 'vQTL', and 'mvQTL', or up to all three.
glm_family	a character vector indicating the GLM family – either 'gaussian' or 'poisson'
return.covar.effects	Should covariate effects estimated at each locus be returned?

Value

27599

Author(s)

Robert W. Corty [e-mail]

Examples

set.seed(27599)
test.cross <- qtl::sim.cross(map = qtl::sim.map(len = rep(20, 5), n.mar = 5), n.ind = 50)
scanonevar(cross = test.cross)

rcorty/vqtl documentation built on May 27, 2019, 3:04 a.m.