import_aeron: Import results from an Aeron run into a list of Fusion...

In stianlagstad/chimeraviz: Visualization tools for gene fusions

Import results from an Aeron run into a list of Fusion objects.

Description

A function that imports the results from an Aeron run into a list of Fusion objects.

Usage

import_aeron(
  filename_fusion_support,
  filename_fusion_transcript,
  genome_version,
  limit
)

Arguments

filename_fusion_support	Filename for the Aeron result file fusion_support..txt.
filename_fusion_transcript	Filename for the Aeron result file fusion_transcripts..txt.
genome_version	Which genome was used in mapping (hg19, hg38, etc.).
limit	A limit on how many lines to read.

Details

Note that the strands and breakpoint positions are not included in the result files from Aeron. These have to be retrieved manually, using the ensembl identifiers (which are included in the result files, and will be available in the Fusion objects after importing).

Value

A list of Fusion objects.

Examples

aeronfusionsupportfile <- system.file(
  "extdata",
  "aeron_fusion_support.txt",
  package="chimeraviz")
aeronfusiontranscriptfile <- system.file(
  "extdata",
  "aeron_fusion_transcripts.fa",
  package="chimeraviz")
fusions <- import_aeron(
  aeronfusionsupportfile,
  aeronfusiontranscriptfile,
  "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.