importStarfusion {chimeraviz}R Documentation

Import results from a STAR-Fusion run into a list of Fusion objects.

Description

A function that imports the results from a STAR-Fusion run, typically from a star-fusion.fusion_candidates.final.abridged file, into a list of Fusion objects.

Usage

importStarfusion(filename, genomeVersion, limit)

Arguments

filename

Filename for the STAR-Fusion star-fusion.fusion_candidates.final.abridged results file.

genomeVersion

Which genome was used in mapping (hg19, hg38, etc.).

limit

A limit on how many lines to read.

Value

A list of Fusion objects.

Examples

starfusionData <- system.file(
  "extdata",
  "star-fusion.fusion_candidates.final.abridged.txt",
  package = "chimeraviz")
fusions <- importStarfusion(starfusionData, "hg19", 3)
# This should import a list of 3 fusions described in Fusion objects.


[Package chimeraviz version 1.4.3 Index]