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Annotate VCF variants with coding changes

Source: R/annotate_coding.r
annotate_coding.Rd

Annotate VCF variants with coding changes

Usage

annotate_coding(vr, txdb, asm)

Arguments

vr

A VRanges object with SNVs and small indels

txdb

TxDb or EnsDb object

asm

Genomic sequence BSGenome object

Value

A GRanges object with annotated variants

Examples

if (interactive()) {
    vcf = system.file("my_variants.vcf", package="pepitope")
    vr = readVcfAsVRanges(vcf)
    txdb = AnnotationHub::AnnotationHub()[["AH100643"]]
    asm = BSgenome.Hsapiens.NCBI.GRCh38::BSgenome.Hsapiens.NCBI.GRCh38
    annotate_coding(vr, txdb, asm)
}