R/hg38_exon_chrom_size.R

In GRIN2: Genomic Random Interval (GRIN)

#' Human GRCh38 Chromosome-Level Exon Target Sizes
#'
#' @description
#' A chromosome-level summary of the total annotated exon target size in the
#' human GRCh38 genome assembly. For each chromosome, the exon lengths from the
#' selected representative transcript of every annotated gene were combined to
#' provide the chromosome-wide exonic search space used in GRIN2 exon-level
#' probability calculations.
#'
#' Representative transcripts were 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 one row per chromosome and 2 columns:
#' \describe{
#'   \item{chrom}{Chromosome identifier.}
#'   \item{size}{Total annotated exon target size on the chromosome in base
#'   pairs, calculated by aggregating the lengths of all exons from the
#'   representative transcript selected for each gene. Representative
#'   transcripts correspond to the MANE Select transcript for protein-coding
#'   genes and the Ensembl canonical transcript for non-protein-coding genes.
#'   This value represents the chromosome-wide exonic target space used in
#'   GRIN2 exon-level probability calculations.}
#' }
#'
#' @details
#' This dataset provides the chromosome-level denominator used for lesion types
#' designated for exon-level analysis in GRIN2. It represents the total exonic
#' target space on each chromosome and is therefore distinct from
#' \code{example_exon_annotation}, which contains exon coordinates for only a
#' subset of genes used in package examples.
#'
#' The dataset should be used together with exon annotations generated from the
#' same genome assembly and representative-transcript selection procedure.
#'
#' @source
#' Derived from human GRCh38 exon annotations retrieved from the Ensembl
#' BioMart database using \code{get.ensembl.annotation()}. Exons were obtained
#' from the MANE Select transcript for protein-coding genes and the Ensembl
#' canonical transcript for non-protein-coding genes. Exon lengths were
#' aggregated for all genes on each chromosome.
#'
#' @usage
#' data(hg38_exon_chrom_size)
#'
#' @keywords datasets
#'
#' @name hg38_exon_chrom_size
#'
#' @docType data
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