import_fusioncatcher: Import results from a Fusioncatcher run into a list of Fusion...

In stianlagstad/chimeraviz: Visualization tools for gene fusions

Import results from a Fusioncatcher run into a list of Fusion objects.

Description

A function that imports the results from a Fusioncatcher run, typically from a final-list-candidate-fusion-genes.txt file, into a list of Fusion objects.

Usage

import_fusioncatcher(filename, genome_version, limit)

Arguments

filename	Filename for the Fusioncatcher final-list-candidate-fusion-genes.txt 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

fusioncatcher833ke <- system.file(
  "extdata",
  "fusioncatcher_833ke_final-list-candidate-fusion-genes.txt",
  package = "chimeraviz")
fusions <- import_fusioncatcher(fusioncatcher833ke, "hg38", 3)
# This should import a list of 3 fusions described in Fusion objects.

stianlagstad/chimeraviz documentation built on Dec. 3, 2023, 8:11 p.m.