get_variants_in_genes: get_variants_in_genes

In frhl/our: genetic data analysis

Description

Returns all variants that are within a gene (defined by start/stop in the reference dataset).

Usage

get_variants_in_genes(df, reference, window = 0)

Arguments

df	data.frame with three columns: chr, bp and id.
reference	a reference dataset that contains 6 columns: ensembl_gene_id, ensembl_transcript_id, hgnc_symbol, chromosome_name, start_position, end_position. This could, for instance be retrieved by biomart.
window	integer. How many bases should the window be extended upstrea/downstream of the gene.

Note

Assumes genes are aligned to positive strand.

Author(s)

flassen

frhl/our documentation built on Feb. 5, 2021, 7:30 p.m.