R/baduel.R

In dearseq: Differential Expression Analysis for RNA-seq data through a robust variance component test

#' 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}}), which is simply a
#'\code{list} with the 3 following components:\itemize{
#'\item \code{genesets}: a \code{list} of \code{n} gene identifiers vectors 
#'composing eachgene set (each gene set is represented as the vector of the 
#'gene identifiers composing it)
#'\item \code{geneset.names}: a vector of length \code{n} containing the gene 
#'set names (i.e. gene sets identifiers)
#'\item{geneset.descriptions}: a vector of length \code{n} containing gene set 
#'descriptions (e.g. textual information on their biological function)
#'}
#'
#'\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
#' if(interactive()){
#' data('baduel_5gs')
#'
#' set.seed(54321)
#' KAvsTBG <- dgsa_seq(exprmat=log2(expr_norm_corr+1),
#'                     covariates=apply(as.matrix(design[,
#'   c('Intercept', 'Vernalized', 'AgeWeeks', 'Vernalized_Population',
#'   'AgeWeeks_Population'), drop=FALSE]), 2, as.numeric),
#'                      variables2test =
#'                          as.matrix(design[, c('PopulationKA'), drop=FALSE]),
#'                      genesets=baduel_gmt$genesets[c(3,5)],
#'                      which_test = 'permutation', which_weights = 'loclin',
#'                      n_perm=1000, preprocessed = TRUE)
#'
#' set.seed(54321)
#' Cold <- dgsa_seq(exprmat=log2(expr_norm_corr+1),
#'                  covariates=apply(as.matrix(design[,
#'    c('Intercept', 'AgeWeeks', 'PopulationKA', 'AgeWeeks_Population'),
#'    drop=FALSE]), 2, as.numeric),
#'                 variables2test=as.matrix(design[, c('Vernalized',
#'                  'Vernalized_Population')]),
#'                  genesets=baduel_gmt$genesets[c(3,5)],
#'                  which_test = 'permutation', which_weights = 'loclin',
#'                  n_perm=1000, preprocessed = TRUE)
#' }
#'
#'
#' @source \url{http://www.ncbi.nlm.nih.gov/bioproject/PRJNA312410}
#'
#' @keywords datasets
#' @docType data
NULL