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Aggregate fusion VCFs into a table

Source: R/annotate_fusions.r
annotate_fusions.Rd

Aggregate fusion VCFs into a table

Usage

annotate_fusions(vr, txdb, asm)

Arguments

vr

A VRanges object with RNA fusions from readVcfAsRanges

txdb

A transcription database, eg. AnnotationHub()[["AH100643"]]

asm

A Genome sequence package object, eg. ::BSgenome.Hsapiens.NCBI.GRCh38

Value

A DataFrame objects with fusions

Examples

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