import_oncofuse: Import results from a oncofuse run into a list of Fusion...

In stianlagstad/chimeraviz: Visualization tools for gene fusions

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

Description

A function that imports the results from a oncofuse run, typically from a results.filtered.tsv file, into a list of Fusion objects.

Usage

import_oncofuse(filename, genome_version, limit)

Arguments

filename	Filename for the oncofuse results .tsv file.
genome_version	Which genome was used in mapping (hg19, hg38, etc.).
limit	A limit on how many lines to read.

Details

This import function was contributed by Lavinia G, ref https://github.com/stianlagstad/chimeraviz/issues/47#issuecomment-409773158

Value

A list of Fusion objects.

Examples

oncofuse833ke <- system.file(
  "extdata",
  "oncofuse.outfile",
  package="chimeraviz")
fusions <- import_oncofuse(oncofuse833ke, "hg19", 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.