select_transcript {chimeraviz} | R Documentation

## Select which transcript to use (for plotting) for a GenePartner object

### Description

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

### Usage

    select_transcript(gene_partner, which_transcripts = "exonBoundary")

### Arguments

`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".

### Details

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.

### Value

A data.frame with transcript data.

### Examples

    # 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))

[Package chimeraviz version 1.16.1 Index]