Create a Manhattan plot with ggplot2.

Create a Manhattan plot using ggplot2 on either RDS or FBM object GWAS results.

pvdiv_manhattan(effects, ind = NULL, snp = NULL, thr = NULL, ncores = 1)

Arguments

effects

Either a gwas effects RDS or FBM object created using 'pvdiv_standard_gwas' (with savetype = "rds" or savetype = "fbm"). If a fbm, this file is saved under the name "gwas_effects_suffix.rds" and can be loaded into R using the bigstatsr function "big_attach".

ind

If effects is a FBM object, this should be the row number of the phenotype from the associated metadata for the FBM object.

snp

If effects is a FBM object, you must also supply a "bigSNP" object; load into R with bigsnpr::snp_attach().

thr

Numeric. Significance threshold plotted as a horizontal line. Default is Bonferroni.

ncores

Integer. Number of cores to use for parallelization.

Value

A ggplot2 plot.