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#' Make a DGEList from tximeta output
#'
#' A simple wrapper function for constructing a DGEList for use with edgeR.
#' See vignette for an example. Requires installation of the edgeR
#' package from Bioconductor.
#'
#' @param se a SummarizedExperiment produced by tximeta
#'
#' @return a DGEList
#'
#' @export
makeDGEList <- function(se) {
if (!requireNamespace("edgeR", quietly=TRUE)) {
stop("this function requires the edgeR package is installed")
}
cts <- assays(se)[["counts"]]
normMat <- assays(se)[["length"]]
normMat <- normMat / exp(rowMeans(log(normMat)))
o <- log(edgeR::calcNormFactors(cts/normMat)) + log(colSums(cts/normMat))
y <- edgeR::DGEList(cts, samples=as.data.frame(colData(se)),
genes=as.data.frame(rowData(se)))
y <- edgeR::scaleOffset(y, t(t(log(normMat)) + o))
y
}
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