manhattan.plot: Create Manhattan plot

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

Create Manhattan plot

Description

Create Manhattan plot

Usage

manhattan.plot(data, traits = NULL, models = NULL, chrom = NULL)

Arguments

data	Variable of class GWASpoly.fitted
traits	Vector of trait names (by default, all traits plotted)
models	Vector of model names (by default, all models plotted)
chrom	optional, to plot only one chromosome

Details

Results for the ref and alt versions of the dominance model are combined. If data is the output from set.threshold, then the threshold is displayed as a horizontal dashed line when models contains a single model. Because the threshold varies between models, it is not drawn when multiple models are included. Although the ref and alt versions of each dominance model are slightly different (as seen with qq.plot), they are treated as a single model for the Manhattan plot, and the average threshold is shown.

Value

ggplot2 object

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