select_transcript: Select which transcript to use (for plotting) for a...

In stianlagstad/chimeraviz: Visualization tools for gene fusions

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))

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