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

In Alice-MacQueen/switchgrassGWAS: Genome Wide Association on Panicum virgatum

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

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.

Alice-MacQueen/switchgrassGWAS documentation built on Jan. 23, 2022, 7:55 p.m.