flanking_sequence: Extract sequence flanking a set of annotations (generally...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Extract sequence flanking a set of annotations (generally coding sequences)

Description

Given a set of annotations and genome, one might want to get the set of adjacent sequences.

Usage

flanking_sequence(
  bsgenome,
  annotation,
  distance = 200,
  type = "gene",
  prefix = ""
)

Arguments

bsgenome	Genome sequence
annotation	Set of annotations
distance	How far from each annotation is desired?
type	What type of annotation is desired?
prefix	Provide a prefix to the names to distinguish them from the existing annotations.

Value

List of sequences before and after each sequence.

See Also

[load_gff_annotations()] [GenomicRanges] [IRanges]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.