GetVariantsInWindow: Get all variants in a specified genomic window

In Simon-Coetzee/funcivar: Calculate overlaps and enrichment between genomic variants and genomic features or segmentations

Description

Import variants from VCF or BED files, optionally restricted to a specific window.

Usage

GetVariantsInWindow(file, position, genome = "hg19", type = "vcf")

Arguments

file	A character vector describing a file to read
position	An optional GRanges object defining the coordinates of the file to import
genome	A character vector describing the genome build against which the variants were mapped e.g. "hg19", "b37", "hg38", "mm10".
type	A character vector stating that the filetype is either 'vcf' or 'bed'

Value

an object of class VCF or GRanges representing the variants

Simon-Coetzee/funcivar documentation built on Aug. 2, 2021, 9:55 a.m.