#' example datasets for documentation #' #' @description example.data is a data list of example datasets. #' There is a dataset example.microarrayData, which is the example of gene expression data of a gene-chip result of \emph{C.elegans}. #' Dataset example.data$ce.bind is a TF binding matrix of ChIP-chip experiment of \emph{C.elegans}. #' Dataset example.data$cd.exprData is expression data of a gene-chip result of \emph{C.elegans}. #' Dataset example.data$hs.bind is a TF binding matrix of ChIP-chip experiment of \emph{H.sapiens}. #' Dataset example.data$hs.exprData is expression data of a combination of a gene-chip result and a RNA-SEQ result of \emph{H.sapiens}. #' #' @format dataframe #' @details #' The dataset example.microarrayData contains columns: ID, logFC, AveExpr, t, P.Value, adj.P.Val, B, genes and symbols. The columns of ID, logFC and symbols are required by GeneNetworkBuilder. #' The dataset example.data$hs.bind contains columns: ID, symbols, logFC and P.Value. #' The dataset example.data$hs.exprData contains columns: from and to. #' #' @docType data #' @keywords data #' @examples #' data(example.data) #' names(example.data) #' head(example.data$example.microarrayData) #' head(example.data$ce.bind) #' head(example.data$ce.exprData) #' head(example.data$hs.bind) #' head(example.data$hs.exprData) #' "example.data" #' C.elegns gene name to wormbase identifier map #' #' map file for converting gene name or sequence name of #' \emph{Caenorhabditis elegans} to wormbase identifier #' #' @format character vector #' @details character vecotr with gene name or sequence name as names and #' wormbase identifier as values. #' @source \url{http://www.wormbase.org/} #' @docType data #' @keywords data #' @examples #' data(ce.IDsMap) #' head(ce.IDsMap) "ce.IDsMap" #' transcript regulatory map of \emph{Caenorhabditis elegans} #' #' transcript regulatory map of \emph{Caenorhabditis elegans} #' #' @format dataframe #' @details transcript regulatory map of \emph{Caenorhabditis elegans} is #' generated using databases edgedb and microCosm Targets. #' @source \url{http://edgedb.umassmed.edu}, \url{http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/} #' @docType data #' @keywords data #' @examples #' data(ce.interactionmap) #' head(ce.interactionmap) #' "ce.interactionmap" #' map file for converting from wormbase identifier to \emph{Caenorhabditis elegans} gene name #' #' map file for converting from wormbase identifier to \emph{Caenorhabditis elegans} gene name #' #' @format character vector #' @details character vecotr with wormbase identifier as names and gene name as values. #' @source \url{http://www.wormbase.org/} #' @docType data #' @keywords data #' @examples #' data(ce.mapIDs) #' head(ce.mapIDs) #' "ce.mapIDs" #' micro RNA of \emph{Caenorhabditis elegans} #' #' micro RNA of \emph{Caenorhabditis elegans} #' #' @format dataframe #' @details The first column is wormbase identifier. And the second column is miRNA names. #' @source \url{http://www.mirbase.org/} #' @docType data #' @keywords data #' @examples #' data(ce.miRNA.map) #' head(ce.miRNA.map) #' "ce.miRNA.map" #' map file for converting gene name or sequence name of \emph{Homo sapiens} to Entrez identifier #' #' map file for converting gene name or sequence name of \emph{Homo sapiens} to Entrez identifier #' #' @format character vector #' @details character vecotr with gene name as names and Entrez identifier as values. #' @docType data #' @keywords data #' @examples #' data(hs.IDsMap) #' head(hs.IDsMap) #' "hs.IDsMap" #' transcript regulation map of \emph{Homo sapiens} #' #' transcript regulation map of \emph{Homo sapiens} #' #' @format dataframe #' @details transcript regulatory map of \emph{Homo sapiens} is generated using #' databases FANTOM, mirGen and microCosm Targets. #' @source \url{http://fantom.gsc.riken.jp/5/}, #' \url{http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/}, #' \url{http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php} #' @docType data #' @keywords data #' @examples #' data(hs.interactionmap) #' head(hs.interactionmap) #' "hs.interactionmap" #' map file for converting from Entrez identifier to \emph{Homo sapiens} gene name #' #' map file for converting from Entrez identifier to \emph{Homo sapiens} gene name #' #' @format character vector #' @details character vecotr with Entrez identifier as names and gene name as values. #' @docType data #' @keywords data #' @examples #' data(hs.mapIDs) #' head(hs.mapIDs) #' "hs.mapIDs" #' micro RNA of \emph{Homo sapiens} #' #' micro RNA of \emph{Homo sapiens} #' #' @format dataframe #' @details The first column is entrez identifier. And the second column is miRNA names. #' @source \url{http://www.mirbase.org/} #' @docType data #' @keywords data #' @examples #' data(hs.miRNA.map) #' head(hs.miRNA.map) #' "hs.miRNA.map"