geposan/R/data.R

#' Information on included species from the Ensembl database.
#'
#' @format A [data.table] with the following columns:
#' \describe{
#'   \item{id}{Unique species ID, these are NCBI taxon IDs}
#'   \item{name}{Human readable species name}
#'   \item{scientific_name}{Scientific name of the species}
#'   \item{table_name}{Table name within the Ensembl database}
#'   \item{n_chromosomes}{Number of chromosomes}
#'   \item{median_chromosome_length}{Median length of chromosomes}
#' }
"species"

#' Information on chromosomes for each included species.
#'
#' @format A [data.table] with the following columns:
#' \describe{
#'   \item{species}{Species ID}
#'   \item{id}{Chromosome ID, theses are Ensembl sequence IDs}
#'   \item{name}{Chromosome name}
#'   \item{length}{Length in base pairs}
#' }
"chromosomes"

#' Information on human genes within the Ensembl database.
#'
#' This includes only genes on the primary suggested assembly of the human
#' nuclear DNA.
#'
#' @format A [data.table] with the following columns:
#' \describe{
#'   \item{id}{Ensembl gene ID}
#'   \item{name}{The gene's HGNC name (if available)}
#'   \item{chromosome}{The human chromosome the gene is located on}
#' }
"genes"

#' Information on gene positions across species.
#'
#' This dataset contains each known value for a gene's distance to the telomeres
#' per species. The data is sourced from Ensembl.
#'
#' @format A [data.table] with the following columns:
#' \describe{
#'   \item{species}{Species ID}
#'   \item{gene}{Gene ID}
#'   \item{chromosome}{Chromosome ID}
#'   \item{start_position}{Start position in base pairs}
#'   \item{end_position}{End position in base pairs}
#'   \item{distance}{Computed distance to nearest telomere}
#' }
"distances"