R/example_exon_annotation.R

In GRIN2: Genomic Random Interval (GRIN)

#' Example Human Exon Annotation Data
#'
#' @description
#' Example human GRCh38 exon annotation data corresponding to all genes included
#' in the \code{hg38_gene_annotation} example dataset. The dataset provides
#' exon-level genomic coordinates that can be used for GRIN2 analyses of
#' genomic lesion types restricted to exonic regions, such as coding single
#' nucleotide variants (SNVs) and small insertions/deletions (indels). Exons
#' were extracted from a single representative transcript for each gene,
#' defined as the MANE Select transcript for protein-coding genes and the
#' Ensembl canonical transcript for non-protein-coding genes.
#'
#' @format A data frame with 5,691 rows and 6 columns:
#' \describe{
#'   \item{gene}{Ensembl gene identifier of the gene to which each annotated
#'   exon belongs.}
#'   \item{chrom}{Chromosome on which the exon is located.}
#'   \item{loc.start}{Exon start position in base pairs.}
#'   \item{loc.end}{Exon end position in base pairs.}
#'   \item{gene_name}{Official gene symbol.}
#'   \item{transcript_exon}{Representative transcript identifier and exon
#'   number (e.g., \code{ENST00000257818_exon1}).}
#' }
#'
#' @source
#' Retrieved from the Ensembl BioMart database using
#' \code{get.ensembl.annotation()} with the "Human-GRCh38" genome assembly
#' (hg38). Exons were obtained from the MANE Select transcript for
#' protein-coding genes and the Ensembl canonical transcript for
#' non-protein-coding genes. The dataset contains exon annotations for all
#' genes included in the \code{hg38_gene_annotation} example dataset.
#'
#' @usage
#' data(example_exon_annotation)
#'
#' @keywords datasets
#'
#' @name example_exon_annotation
#'
#' @docType data
NULL