select_transcript {chimeraviz} | R Documentation |
This function takes a GenePartner object and creates a transcript data.frame with transcript information, including only the transcripts given by the parameter which_transcripts
select_transcript(gene_partner, which_transcripts = "exonBoundary")
gene_partner |
The GenePartner object to select a transcript for. |
which_transcripts |
This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary". |
select_transcript() selects which transcript to create by this prioritization:
1. Exon boundary transcripts. 2. Within exon transcripts. 3. Within intron transcripts. 4. Intergenic transcripts.
A data.frame with transcript data.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Get transcripts fusion <- get_transcripts_ensembl_db(fusion, edb) # Select transcript transcriptsA <- select_transcript(upstream_partner_gene(fusion))