R/filter_genes.R

In alexvpickering/rkal: Run, Import, and Export 'kallisto' Quantifications

#' Filter genes in RNA-seq ExpressionSet
#'
#' Uses \link[edgeR]{filterByExpr} to filter based on 'counts' assay or 'exprs'
#' assay if 'counts' isn't available (for ARCHS4 data).
#'
#'
#' @param eset ExpressionSet with 'counts' assayDataElement and group column in
#'  pData
#'
#' @return filtered \code{eset}
#' @export
#' @seealso \link[edgeR]{filterByExpr}
#'
filter_genes <- function(eset) {
    els <- Biobase::assayDataElementNames(eset)
    els <- ifelse("counts" %in% els, "counts", "exprs")
    counts <- Biobase::assayDataElement(eset, els)

    keep <- edgeR::filterByExpr(counts, group = eset$group)
    eset <- eset[keep, ]
    if (!nrow(eset)) stop("No genes with reads after filtering")
    return(eset)
}