get_transcripts_ensembl_db: Retrieves transcripts for partner genes in a Fusion object...

In stianlagstad/chimeraviz: Visualization tools for gene fusions

Retrieves transcripts for partner genes in a Fusion object using Ensembldb

Description

This function will retrieve transcripts for both genes in a fusion. It will check all transcripts and decide for each transcript if the fusion breakpoint happens at 1) an exon boundary, 2) within an exon, or 3) within an intron. This is done because fusions happening at exon boundaries are more likely to produce biologically interesting gene products. The function returns an updated Fusion object, where the fusion@gene_upstream@transcriptsX slots are set with transcript information.

Usage

get_transcripts_ensembl_db(fusion, edb)

Arguments

fusion	The fusion object to find transcripts for.
edb	The edb object used to fetch data from.

Value

An updated fusion object with transcript data stored.

Examples

# Load fusion data and choose a fusion object:
defuseData <- system.file(
  "extdata",
  "defuse_833ke_results.filtered.tsv",
  package="chimeraviz")
fusions <- import_defuse(defuseData, "hg19", 1)
fusion <- get_fusion_by_id(fusions, 5267)
# Create edb object
edbSqliteFile <- system.file(
  "extdata",
  "Homo_sapiens.GRCh37.74.sqlite",
  package="chimeraviz")
edb <- ensembldb::EnsDb(edbSqliteFile)
# Add transcripts data to fusion object
fusion <- get_transcripts_ensembl_db(fusion, edb)
# The transcripts are now accessible through fusion@gene_upstream@transcripts and
# fusion@gene_downstream@transcripts .

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