R/cll-data.R

In reimandlab/ActiveDriverWGSR: A Driver Discovery Tool for Cancer Whole Genomes

#' CLL mutations
#'
#' CLL whole genome simple somatic mutations from Alexandrov et, 2013
#'
#' @name cll_mutations
#'
#' @docType data
#'
#' @usage data(cll_mutations)
#'
#' @format A data frame containing the following columns: chr, pos1, pos2, ref, alt, patient.
#' \describe{
#'     \item{chr}{autosomal chromosomes as chr1 to chr22 and sex chromosomes as chrX and chrY}
#'     \item{pos1}{the start position of the mutation in base 1 coordinates}
#'     \item{pos2}{the end position of the mutation in base 1 coordinates}
#'     \item{ref}{the reference allele as a string containing the bases A, T, C or G}
#'     \item{alt}{the alternate allele as a string containing the bases A, T, C or G}
#'     \item{patient}{the patient identifier as a string}
#' }
#'
#' @keywords datasets
#'
#' @references Alexandrov, Ludmil B., et al. "Signatures of mutational processes in human cancer." Nature 500.7463 (2013): 415.
#' (\href{https://pubmed.ncbi.nlm.nih.gov/23945592/}{PubMed})
#'
#' @source \href{https://www.nature.com/articles/nature12477}{Publication}
#'
#' @examples
#' data(cll_mutations)
#' \donttest{
#' data(cancer_genes)
#' ActiveDriverWGS(mutations = cll_mutations, elements = cancer_genes)
#' }
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