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

In chimeraviz: Visualization tools for gene fusions

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

import_starfusion(filename, genome_version, limit)

Arguments

filename	Filename for the STAR-Fusion star-fusion.fusion_candidates.final.abridged results file.
genome_version	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 <- import_starfusion(starfusionData, "hg19", 3)
# This should import a list of 3 fusions described in Fusion objects.

chimeraviz documentation built on Jan. 19, 2021, 2 a.m.