R/exampleData.R

In NelleV/moanin: An R Package for Time Course RNASeq Data Analysis

#' Small data set for running examples
#'
#' @name exampleData
#' @docType data
#' @format Three objects are loaded, a data frame of expression of 500 genes by
#'   84 samples (\code{testData}), a data frame with meta information on those
#'   84 samples (\code{testMeta}), and a data frame giving the GOID of the genes
#'   in \code{testData}.
#' @details This data is a subset of the full time course data available as
#'   \code{\link[timecoursedata]{shoemaker2015}} and is only provided for the
#'   purpose of running examples, and not for biological meaning. Users should
#'   refer to the full data set.
#' @details The rownames of \code{testData} are RefSeq. 
#' @keywords data
#' @aliases testData testMeta testGenesGO
#' @examples
#' #code used to create data:
#' \dontrun{
#' library(timecoursedata)
#' data(shoemaker2015)
#' testData<-shoemaker2015$data[1:500,]
#' whSamples<-which(shoemaker2015$meta$Group %in% c("C","K","M"))
#' testData<-testData[,whSamples]
#' testMeta<-droplevels(shoemaker2015$meta[whSamples,])
#' library(biomaRt)
#' ensembl = useMart("ensembl")
#' ensembl = useMart("ensembl")
#' ensembl = useDataset("mmusculus_gene_ensembl", mart=ensembl)
#' testGenesGO = getBM(attributes=c("go_id", "refseq_mrna"),
#'               values=rownames(testData),
#'               filters="refseq_mrna",
#'               mart=ensembl)
#' save(list=c("testData","testMeta","testGenesGO"),file="data/exampleData.rda")
#' }
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