GWASpoly: Compute marker significance scores

In jendelman/GWASpoly: Genome-wide Association Studies for Autopolyploids

Compute marker significance scores

Description

Compute marker significance scores

Usage

GWASpoly(data, models, traits = NULL, params = NULL, n.core = 1, quiet = F)

Arguments

data	Output from set.K
models	Vector of model names
traits	Vector trait names (by default, all traits)
params	Optional list of params created by set.params
n.core	Number of cores for parallel computing
quiet	TRUE/FALSE whether to suppress output charting progress

Details

The following marker-effect models are available:

• "additive": Indicates the marker effect is proportional to the dosage of the alternate allele

• "X-dom": where X can be any integer between 1 and ploidy/2 and refers to the allele dosage needed for complete dominance (e.g., "1-dom" = simplex dominance, "2-dom" = duplex dominance). The software tries both dominance patterns for a given dosage model, e.g., whether the reference or alternate allele is dominant

• "diplo-general": All heterozygotes have the same effect

• "diplo-additive": All heterozygotes have the same effect, constrained to be halfway between the homozygous effects

• "general": There are no constraints on the effects of the different dosage levels

To specify additional model parameters, such as the inclusion of fixed effects (Q matrix) and the minimum minor allele frequency, use set.params

Value

Variable of class GWASpoly.fitted

jendelman/GWASpoly documentation built on Oct. 16, 2024, 5:59 a.m.