R/GMD-data.R

In GMD: Generalized Minimum Distance of distributions

##' Transcription Start Site Distributions (TSSDs) by CAGE tags. 
##' 
##' \code{cage} is a list of 20 named TSSDs.
##' \code{cagel} is a longer version of \code{\link{cage}}, with 50 named TSSDs.
##' @name cage
##' @aliases cage cagel
##' @title CAGE Data: Transcription Start Site Distributions (TSSDs) by CAGE tags
##' @docType data
##' @usage
##' cage
##' cagel
##' @references Zhao et al (2011),
##' "Systematic Clustering of Transcription Start Site Landscapes",
##' \emph{PLoS ONE} \bold{6}(8): e23409.
##' 
##' \url{http://dx.plos.org/10.1371/journal.pone.0023409}
##' @seealso \code{\link{gmdp}} and \code{\link{gmdm}}, with examples using \code{\link{cage}}. \code{\link{chipseq}} for histone marks by ChIP-seq reads.
##' @keywords datasets
##' @examples
##' help(cage)
##' data(cage)
##' class(cage)
##' length(cage)
##' names(cage)
##' \dontrun{cage}
##' 
##' data(cagel)
##' names(cagel)
##' \dontrun{cagel}
NULL



##' The Distributions of Histone Modification Enrichment (and Others) by ChIP-seq reads that are binned,
##' aligned and averaged around +/-5000nt of Transcription Start Sites (TSSs) of scattered-type TSSDs
##' (see References).
##' 
##' \code{chipseq_mES} is a list of 6 named ChIP-seq read distributions from mouse ES cells.\cr
##' \code{chipseq_hCD4T} is a list of 40 named ChIP-seq read distributions from human CD4+ T cells.\cr
##' @name chipseq
##' @aliases chipseq chipseq_mES chipseq_hCD4T
##' @title ChIP-seq data: ChIP-seq Enrichment around TSSs
##' @docType data
##' @usage
##' chipseq_mES
##' chipseq_hCD4T
##' @references Zhao et al (2011),
##' "Systematic Clustering of Transcription Start Site Landscapes",
##' \emph{PLoS ONE} \bold{6}(8): e23409.
##' 
##' \url{http://dx.plos.org/10.1371/journal.pone.0023409}
##' @seealso \code{\link{gmdp}} and \code{\link{gmdm}}, with examples using \code{\link{chipseq}}. \code{\link{cage}} for data of Transcription Start Sites (TSSs) by CAGE tags.
##' @keywords datasets
##' @examples
##' require(GMD)
##' help(chipseq)
##' data(chipseq_mES)
##' class(chipseq_mES)
##' length(chipseq_mES)
##' names(chipseq_mES)
##' \dontrun{chipseq_mES}
##' 
##' data(chipseq_hCD4T)
##' names(chipseq_hCD4T)
NULL