Get up and downstream sequences of variant(s) and store in VRanges metadata

Finds nucleotides up and downstream of a variant within a genome and store within upstream and downstream fields in the metadata of the supplied VRanges object.

Usage

getFlankingSeqs(x, up, down, bs_genome_obj, allele = NULL)

Arguments

x

A VRanges or GRanges object with one or more variants. seqnames and ranges fields are required.

up

Numeric, number of bases to return upstream of variant

down

Numeric, number of bases to return downstream of variant

bs_genome_obj

A BSgenome object for the genome build to use.

allele

Column name in meta data storing allele

Value

a VRanges object with metadata columns upstream and downstream.