#' @title Compute TAI or TDI Profiles Omitting a Given Gene
#' @description For each gene i, exclude the corresponding gene i from the global
#' PhyloExpressionSet or DivergenceExpressionSet and compute the \code{\link{TAI}} or \code{\link{TDI}}
#' profile for the corresponding global PhyloExpressionSet or DivergenceExpressionSet
#' with excluded gene i.
#'
#' This procedure results in a TAI or TDI profile Matrix storing the TAI or TDI profile for each omitted gene i.
#' @param ExpressionSet a standard PhyloExpressionSet or DivergenceExpressionSet object.
#' @return a numeric matrix storing TAI or TDI profile for each omitted gene i.
#' @author Hajk-Georg Drost
#' @examples
#'
#' # read standard phylotranscriptomics data
#' data(PhyloExpressionSetExample)
#' data(DivergenceExpressionSetExample)
#'
#' # example PhyloExpressionSet
#' omMatrix_ps <- omitMatrix(PhyloExpressionSetExample)
#'
#' # example DivergenceExpressionSet
#' omMatrix_ds <- omitMatrix(DivergenceExpressionSetExample)
#'
#'
#' @export
omitMatrix <- function(ExpressionSet)
{
ExpressionSet <- as.data.frame(ExpressionSet)
is.ExpressionSet(ExpressionSet)
ncols <- dim(ExpressionSet)[2]
oMatrix <- matrix(NA_real_, ncol = (ncols - 2), nrow = nrow(ExpressionSet))
oMatrix <- cpp_omitMatrix(as.matrix(ExpressionSet[ , 3:ncols]),as.vector(ExpressionSet[ , 1]))
colnames(oMatrix) <- names(ExpressionSet)[3:ncols]
rownames(oMatrix) <- paste0("(-) ",ExpressionSet[ , 2])
return(oMatrix)
}
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