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Can be called once and the result passed to PlotGene() or PlotRegion() to avoid repeated downloads.

Source: R/GN_LoadGTF.R
LoadGTF.Rd

Can be called once and the result passed to PlotGene() or PlotRegion() to avoid repeated downloads.

Usage

LoadGTF(species = "Human", file = NULL)

Arguments

species

Species to load annotation for: "Human" or "Mouse".

file

Optional file path to a local GTF file. If provided, imports directly without connecting to AnnotationHub.

Value

A data frame containing GTF annotation with columns including seqnames, start, end, strand, type, gene_id, gene_name, transcript_id, etc.

Details

Loading annotations from AnnotationHub can take time on first use. By calling this function separately, you can:

  • Load the annotation once and reuse it across multiple plots

  • Save the annotation to disk for faster future sessions

Human annotations use Ensembl GTF (AH110867). Mouse annotations use Ensembl GTF (AH47076).

Examples

if (FALSE) { # \dontrun{
  # Load human GTF once
  gtf <- LoadGTF(species = "Human")

  # Optionally save for future sessions
  saveRDS(gtf, "human_gtf.rds")

  # Use in multiple plots without reloading
  PlotGene(bed = bed, geneID = "TP53", gtf = gtf)
  PlotGene(bed = bed, geneID = "BRCA1", gtf = gtf)

  # Load from saved file in future sessions
  gtf <- readRDS("human_gtf.rds")
} # }