decide_transcript_category | R Documentation |
This function will check where in the transcript (the GRanges object) the fusion breakpoint is located, and return either "exonBoundary", "withinExon", "withinIntron", or "intergenic".
decide_transcript_category(gr, fusion)
gr |
The GRanges object containing the transcript to be checked. |
fusion |
The fusion object used to check the transcript. |
Either "exonBoundary", "withinExon", "withinIntron", or "intergenic" depending on where in the transcript the breakpoint hits.
# 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) # Get all exons for all transcripts in the genes in the fusion transcript allTranscripts <- ensembldb::exonsBy( edb, filter = list( AnnotationFilter::GeneIdFilter( c( partner_gene_ensembl_id(upstream_partner_gene(fusion)), partner_gene_ensembl_id(downstream_partner_gene(fusion))))), columns = c( "gene_id", "gene_name", "tx_id", "tx_cds_seq_start", "tx_cds_seq_end", "exon_id")) # Extract one of the GRanges objects gr <- allTranscripts[[1]] # Check where in the transcript the fusion breakpoint hits decide_transcript_category(gr, fusion) # "exonBoundary" # Check another case gr <- allTranscripts[[3]] decide_transcript_category(gr, fusion) # "withinIntron"
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