get_transcripts_ensembl_db {chimeraviz} | R Documentation |
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.
get_transcripts_ensembl_db(fusion, edb)
fusion |
The fusion object to find transcripts for. |
edb |
The edb object used to fetch data from. |
An updated fusion object with transcript data stored.
# 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 .