write_fusion_reference: Write fusion junction sequence to a fasta file

In stianlagstad/chimeraviz: Visualization tools for gene fusions

Write fusion junction sequence to a fasta file

Description

This function will write the fusion sequence to a fasta file, using Biostring::writeXStringSet() .

Usage

write_fusion_reference(fusion, filename)

Arguments

fusion	The Fusion object we want to create a fasta file from.
filename	The filename to write to.

Value

Writes the fusion junction sequence to the given filename.

Examples

# Import the filtered defuse results
defuse833keFiltered <- system.file(
  "extdata",
  "defuse_833ke_results.filtered.tsv",
  package="chimeraviz")
fusions <- import_defuse(defuse833keFiltered, "hg19", 1)
# Get a specific fusion
fusion <- get_fusion_by_id(fusions, 5267)
# Create temporary file to hold the fusion sequence
fastaFileOut <- tempfile(pattern = "fusionSequence", tmpdir = tempdir())
# Write fusion sequence to file
write_fusion_reference(fusion, fastaFileOut)

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