Plot a GWAS scan (Manhattan or QQ)

Plot a GWAS scan (Manhattan or QQ)

Usage

# S3 method for class 'gs_gwas'
plot(x, type = c("manhattan", "qq"), alpha = 0.05, ...)

Arguments

x

A gs_gwas object from gwas().

type

"manhattan" (default) or "qq".

alpha

Genome-wide significance level for the Bonferroni line on the Manhattan plot (default 0.05).

...

Further graphical parameters passed to graphics::plot().

Value

The gs_gwas object, invisibly.

Examples

sim <- simulate_population(n = 150, m = 500, n_qtl = 10, h2 = 0.6, seed = 1)
scan <- gwas(sim$pheno, sim$geno, n_pc = 3)
plot(scan)

plot(scan, type = "qq")