decide_transcript_category: 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 check where in the transcript (the GRanges object) the fusion breakpoint is located, and return either "exonBoundary", "withinExon", "withinIntron", or "intergenic".

Usage

decide_transcript_category(gr, fusion)

Arguments

gr	The GRanges object containing the transcript to be checked.
fusion	The fusion object used to check the transcript.

Value

Either "exonBoundary", "withinExon", "withinIntron", or "intergenic" depending on where in the transcript the breakpoint hits.

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)
# 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"

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