decide_transcript_category {chimeraviz} | R Documentation

## 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"

[Package chimeraviz version 1.12.3 Index]