Plot the -log10p-value distributions for two univariate GWAS against one another using ggplot.

This function takes GWAS results from the dive_ functions of snpdiver that create FBM of univariate GWAS effects. It creates a dataframe from these results suitable for an Upset plot, containing only the rows/SNPs significant in at least one univariate GWAS at the -log10p threshold specified.

pvdiv_fbm_upset_df(effects, snp, metadata, thr = 7, quantile = NA, ncores = NA)

Arguments

effects

fbm created using 'pvdiv_standard_gwas'. Saved under the name "gwas_effects_suffix.rds" and can be loaded into R using the bigstatsr function "big_attach".

snp

A "bigSNP" object; load with bigsnpr::snp_attach(). Here, genomic information for Panicum virgatum.

metadata

Metadata created using 'pvdiv_standard_gwas'. Saved under the name "gwas_effects_suffix_associated_metadata.csv"

thr

Numeric. Threshold above which SNP/row is kept for comparisons.

quantile

Numeric. Top quantile/percentile to keep for each GWAS for comparisons.

ncores

Numeric. Number of cores used for fbm functions. Default is nb_cores() from bigstatsr.