R/genomeInfo-data.R

In derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

#' Genome samples information
#'
#' Information for the 31 samples downloaded from the Short Read Archive from
#' studies comparing CEU and YRI populations. This data is used to specify the
#' adjustment variables in [calculateStats]. The data is sorted according
#' to the BAM files identifiers. Reads were 36bp long.
#'
#' @details The samples are from:
#' \describe{
#' \item{10 }{ unrelated females from the YRI population.}
#' \item{5 }{ unrelated females from the CEU population.}
#' \item{5 }{ unrelated males (unrelated to the females too) from the CEU
#' population.}
#' }
#'
#' @references
#' 1. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E,
#' Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms
#' underlying human gene expression variation with RNA sequencing. Nature 2010
#' Apr.
#'
#' 2. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett
#' J, Guigo R, Dermitzakis ET. Transcriptome genetics using second generation
#' sequencing in a Caucasian population. Nature 2010 Mar.
#'
#' @name genomeInfo
#' @docType data
#' @format  A data.frame with 5 columns:
#' \describe{
#' \item{run }{ The short name used to identify the sample BAM file.}
#' \item{library.layout }{ Whether it was a single-end library or a paired-end
#' library.}
#' \item{hapmap.id }{ The HapMap identifier of the person sequenced. Note that
#' some were sequenced more than once.}
#' \item{gender }{ Whether the person sequence is a female or a male.}
#' \item{pop }{ The population the person belongs to.}
#' }
#' @keywords datasets
#' @seealso [genomeData], [calculateStats]
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