variant_features: annotate variants with features from gff

In greymonroe/polymorphology: Functions from Monroe et al 2022

annotate variants with features from gff

Description

annotate variants with features from gff

Usage

variant_features(vcf, gff, type, ann = "info", window = 0)

Arguments

vcf	data.table object of variant data (data.table with CHROM, POS, REF, and ALT columns)
gff	data.table object of gff data (data.table with "chr","source","type","start","stop","V1","direction","V2","info" columns)
type	type of feature (e.g, "CDS","gene", etc)
ann	which column to annotate with (values will be concatenated to track the names of the features a varint is found in), default is "info" column of gff
window	number of base pairs to expand (e.g. to include regions +- 3000 base pairs from feature you set 3000)

Value

a vector of pasted (" AND " delimited) annotations (based on column provided by ) for each feature the variant is found in

greymonroe/polymorphology documentation built on Aug. 6, 2023, 1:33 a.m.