R/documented_data.R

In daewoooo/breakpointRdata: Strand-seq data for demonstration purposes

#' Example BAM-files
#'
#' A set of BAM-files for demonstration purposes of the functions in package \pkg{breakpointR}.
#'
#' @docType data
#' @name example_bams
#' @aliases bams
#' @format A BAM files with aligned reads with one read per line.
#' @details BAM files contain single-end reads aligned to GRCh38 reference genome. \cr
#' Read sequences and quality values have been removed in order to reduce the file size.
#' @source A lyphoblastoid cell line of Puerto Rican origin (HG00731). Raw reads were aligned to the GRCh38/hg38 reference assembly. The file has been downsampled to 20\% of the coverage to reduce the file size. 
#' @references \url{https://www.biorxiv.org/content/early/2017/09/23/193144}
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#' Results for example BAM-files
#'
#' Localized breakpoints in example BAM-files, generated by the \pkg{breakpointR} package. 
#'
#' @docType data
#' @name example_results
#' @aliases results
#' @format Files containing \code{BreakPoint} object.
#' @details 
#' A \code{BreakPoint} object is a \code{list} containing given elements: ID, fragments, deltas, breaks, confint, counts, lib.metrics and params.
#' \itemize{
#'    \item ID - unique identifier for a given library.
#'    \item fragments - A \code{GRanges-class} object that stores analyzed sequencing reads.
#'    \item deltas - A \code{GRanges-class} object that stores binned minus reads differences.
#'    \item breaks - A \code{GRanges-class} object that stores localized breaks.
#'    \item confint - A \code{GRanges-class} object that stores confidence intervals around localized breaks.
#'    \item counts - A \code{GRanges-class} object that stores directional read counts in between localized breaks.
#'    \item lib.metrics - A named \code{vector} with some useful library metrics.
#'    \item params - A named \code{vector} with user defined parameters used to run \pkg{breakpointR} package.
#' }
#' @source A lyphoblastoid cell line of Puerto Rican origin (HG00731). Raw reads were aligned to the GRCh38/hg38 reference assembly.
#' @references \url{https://www.biorxiv.org/content/early/2017/09/23/193144}
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