R/pTDI.R

Defines functions pTDI

Documented in pTDI

#' @title Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence Index
#' @description This function takes a standard \emph{ExpressionSet} object and computes the partial contribution of the different divergence strata (ds) to the global Transcriptome Divergence Index profile.
#' @param ExpressionSet a standard DivergenceExpressionSet object.
#' @author Hajk-Georg Drost
#' @details This function (\code{pTDI}) computes the partial TDI contribution for each phylostratum and each developmental stage and returns a data matrix storing the partial TDI contribution value for each divergence and each developmental stage. 
#' 
#' @examples
#' 
#' data(DivergenceExpressionSetExample)
#' 
#' # get the partial contribution of divergence strata to the global
#' # TDI pattern
#' pTAI(DivergenceExpressionSetExample)
#' 
#' @references 
#' Domazet-Loso T. and Tautz D. (2010). \emph{A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns}. Nature (468): 815-818.
#' 
#' Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.
#' 
#' Drost HG et al. (2015). Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012.
#' @seealso \code{\link{pTAI}}, \code{\link{TAI}}, \code{\link{TDI}}, \code{\link{PlotPattern}}
#' @export
pTDI <- function(ExpressionSet){
        
        apply(pStrata(ExpressionSet),2,cumsum)
        
}
HajkD/myTAI documentation built on Oct. 13, 2023, 12:07 a.m.