R/CopyNeutralIMA.R

In xpastor/CopyNeutralIMA: Copy Neutral Illumina Methylation Arrays

#' Reference samples for analysis of IlluminaHumanMethylation arrays.
#'
#' The CopyNeutralIMA package provides a set of 51 samples for
#' IlluminaHumanMethylation450k arrays and a set of 13 samples for
#' IlluminaHumanMethylationEPIC arrays.
#'
#' The package includes two RGChannelSetExtended objects, one with 51 samples
#' hybridized with the IlluminaHumanMethylation450k array and another one with
#' 13 samples hybridized with the IlluminaHumanMethylationEPIC array.
#'
#' For the 450k arrays, samples from GEO series 
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49618}{GSE49618}
#' \insertCite{GSE49618}{CopyNeutralIMA}, 
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61441}{GSE61441} 
#' \insertCite{GSE61441}{CopyNeutralIMA} and 
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106089}{GSE106089} 
#' \insertCite{GSE106089}{CopyNeutralIMA} are provided.
#'
#' For the EPIC arrays, samples from GEO series 
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86831}{GSE86831}/
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86833}{GSE86833} #' \insertCite{GSE86831}{CopyNeutralIMA}, 
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98990}{GSE98990} 
#' \insertCite{GSE98990}{CopyNeutralIMA} and 
#' \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100825}{GSE100825} 
#' \insertCite{GSE100825}{CopyNeutralIMA} are also provided.
#'
#' The provided samples consist of material from healthy patients with nominally
#' no copy number aberrations.
#'
#' Users may use this data package as controls for their copy number profiling 
#' analysis or for testing other tools.
#'
#' Check the vignette on how to use these data as control samples for 
#' \pkg{conumee}.
#'
#' @importFrom Rdpack reprompt
#'
#' @references
#'     \insertAllCited{}
"_PACKAGE"