sanity_check: Sanity checks on GWAS dataframes

In locuszoomr: Gene Locus Plot with Gene Annotations

Sanity checks on GWAS dataframes

Description

Performs sanity checks on GWAS dataframes to check similar chromosome content, overlap in SNP ids and alignment of SNPs by chromosome/position.

Usage

sanity_check(data, data2, chrom = NULL, pos = NULL, p = NULL, labs = NULL)

Arguments

data	Dataframe of GWAS results with columns for chromosome, position, p value and SNP rs IDs. Data.tables are coerced to dataframe.
data2	Dataframe of 2nd GWAS results for comparison.
chrom	Vector determines which column in data and data2 contains chromosome information. If NULL or NA tries to autodetect the columns. The 1st element refers to data and 2nd element refers to data2.
pos	Determines which column in data and data2 contains position information. See chrom.
p	Determines which column in data and data2 contains SNP p-values. See chrom.
labs	Determines which column in data and data2 contains SNP rs IDs. See chrom.

Value

No return value. Prints diagnostic messages.

locuszoomr documentation built on Oct. 9, 2026, 5:06 p.m.