big_upset_df: Plot the -log10p-value distributions for two univariate GWAS...

In Alice-MacQueen/snpdiver: Explore SNP Effects on Multiple Phenotypes in Diversity Panels

Description

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.

Usage

big_upset_df(effects, thr = 7, quantile = NA, metadata, ncores = nb_cores)

Arguments

effects	fbm created using 'dive_phe2effects' or 'dive_phe2mash'. Saved under the name "gwas_effects_suffix.rds" and can be loaded into R using the bigstatsr function "big_attach".
thr	Numeric. Threshold above which SNP/row is kept for comparisons.
quantile	Numeric. Top quantile/percentile to keep for each GWAS for comparisons.
metadata	Metadata created using 'dive_phe2effects' or 'dive_phe2mash'. Saved under the name "gwas_effects_suffix_associated_metadata.csv".
ncores	Optional integer to specify the number of cores to be used for parallelization. You can specify this with bigparallelr::nb_cores().

Alice-MacQueen/snpdiver documentation built on Dec. 17, 2021, 8:41 a.m.