Nothing
#' Small portion of RNA-seq data from plant physiology study.
#'
#'A subsample of the RNA-seq data from Baduel \emph{et al.} studying Arabidopsis Arenosa physiology.
#'
#'@name baduel_5gs
#'@rdname baduel_5gs
#'@aliases baduel baduel_5gs baduel_gmt design expr_norm_corr
#'
#'@usage data(baduel_5gs)
#'
#'@references Baduel P, Arnold B, Weisman CM, Hunter B & Bomblies K (2016).
#'Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis
#'Arenosa. \emph{Plant Physiology}, 171(1):437-51. \href{https://doi.org/10.1104/pp.15.01875}{10.1104/pp.15.01875}.
#'@references Agniel D & Hejblum BP (2017). Variance component score test for
#'time-course gene set analysis of longitudinal RNA-seq data, \emph{Biostatistics},
#'18(4):589-604. \href{https://doi.org/10.1093/biostatistics/kxx005}{10.1093/biostatistics/kxx005}.
#'\href{https://arxiv.org/abs/1605.02351}{arXiv:1605.02351}.
#'
#'@format 3 objects\itemize{
#'\item{\code{design}:} a design matrix for the 48 measured samples, containing the following variables:\itemize{
#' \item \code{SampleName} corresponding column names from \code{expr_norm_corr}
#' \item \code{Intercept} an intercept variable
#' \item \code{Population} a factor identifying the plant population
#' \item \code{Age_weeks} numeric age of the plant at sampling time (in weeks)
#' \item \code{Replicate} a purely technical variable as replicates are not from the same individual over weeks.
#' Should not be used in analysis.
#' \item \code{Vernalized} a logical variable indicating whether the plant had undergone
#' vernalization (exposition to cold and short day photoperiods)
#' \item \code{Vernalized} a binary variable indicating whether the plant belonged to the KA
#' population
#' \item \code{AgeWeeks_Population} interaction variable between the \code{AgeWeeks} and
#' \code{Population} variables
#' \item \code{AgeWeeks_Vernalized} interaction variable between the \code{AgeWeeks} and
#' \code{Vernalized} variables
#' \item \code{Vernalized_Population} interaction variable between the \code{Vernalized} and
#' \code{Population} variables
#' \item \code{AgeWeeks_Vernalized_Population} interaction variable between the \code{AgeWeeks},
#' \code{Vernalized} and \code{Population} variables
#'}
#'\item{\code{baduel_gmt}:} a \code{gmt} object containing 5 gene sets of interest (see \code{\link[GSA:GSA.read.gmt]{GSA.read.gmt}})
#'\item{\code{expr_norm_corr}:} a numeric matrix containing the normalized batch corrected expression
#'for the 2454 genes included in either of the 5 gene sets of interests
#'}
#'
#'@examples
#' \dontrun{
#' rm(list=ls())
#' data("baduel_5gs")
#'
#' set.seed(54321)
#' KAvsTBG <- tcgsa_seq(y=log2(expr_norm_corr+1), x=apply(as.matrix(design[, c("Intercept",
#' "Vernalized", "Age_weeks", "Vernalized_Population", "AgeWeeks_Population"), drop=FALSE]),
#' 2, as.numeric),
#' phi=as.matrix(design[, c("PopulationKA"), drop=FALSE]),
#' genesets=baduel_gmt$genesets[c(3,5)],
#' which_test = "permutation", which_weights = "loclin",
#' n_perm=1000, preprocessed = TRUE, doPlot = TRUE)
#'
#' set.seed(54321)
#' Cold <- tcgsa_seq(y=log2(expr_norm_corr+1), x=apply(as.matrix(design[, c("Intercept",
#' "Age_weeks", "PopulationKA", "AgeWeeks_Population"), drop=FALSE]), 2, as.numeric),
#' phi=as.matrix(design[, c("Vernalized", "Vernalized_Population")]),
#' genesets=baduel_gmt$genesets[c(3,5)],
#' which_test = "permutation", which_weights = "loclin",
#' n_perm=1000, preprocessed = TRUE, doPlot = TRUE)
#' }
#'
#'
#' @source \url{https://www.ncbi.nlm.nih.gov/bioproject/PRJNA312410/}
#'
#' @keywords datasets
#' @docType data
NULL
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.