get_overlapping_genes: Find genes that overlap with a SNP.

In Gregor-Mendel-Institute/gwaR: A collection of R functions to conduct GWAS analysis (in Arabidopsis thaliana)

Find genes that overlap with a SNP.

Description

Find genes that overlap with a SNP.

Usage

get_overlapping_genes(gwas_table = NULL, n_hit = 1, distance = -1)

Arguments

gwas_table	Object returned from format_gwas function
n_hit	The number of SNPs that should be looked up.
distance	The maximum distance from SNP to annotation, can be varied to lookup genes within a specific distance

Details

Based on a GWAS table, returns the gene annotation that is overlapping with each SNP for the number of SNP specified. If there is no overlap, the SNP is returned, but the GeneID column is empty. Lookup is done via ensembl plants; requires internet connection.

See Also

format_gwas

get_nearest_genes

Gregor-Mendel-Institute/gwaR documentation built on Feb. 8, 2023, 8:34 p.m.