fit.QTL: Test markers as QTL under backward elimination

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

Test markers as QTL under backward elimination

Description

Test markers as QTL under backward elimination

Usage

fit.QTL(data, trait, qtl, fixed = NULL)

Arguments

data	variable inheriting from class GWASpoly.K
trait	name of trait
qtl	data frame to specify the multi-QTL model (see Details)
fixed	data frame to specify the fixed effects (see Details)

Details

qtl is a data frame with columns "Marker" and "Model", where each row corresponds to a QTL. fixed is a data frame with columns "Effect" and "Type": the first column is the name of the effect, which must match a column in the phenotype input file, and the second column is either "factor" or "numeric". The p-value and R2 for each marker are based on the likelihood ratio test under backward elimination, comparing the deviance to the chi-squared distribution.

Value

data frame with partial r2 and p-values

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