createGeneAnnotation: Create gene annotation object

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Create gene annotation object

Description

Create gene annotation object

Usage

createGeneAnnotation(
  window,
  TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene,
  longest = TRUE
)

Arguments

window	GRanges object with coordinates to use for selecting the genes to plot.
TxDb	TxDb object to use for drawing the genomic annotation.
longest	Logical indicating whether to plot only the longest transcripts for each gene in the gene annotation plot.

Value

GRanges object with the gene annotation in the window.

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
window <- GRanges("chr16:11298262-11400036")
gene_anno <- createGeneAnnotation(
    window = window,
    TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene
)

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.