R/topGenes.R

In PYangLab/Cepo: Cepo for the identification of differentially stable genes

#' @title Extract the top genes from the Cepo output
#' @param object Output from the Cepo function
#' @param n Number of top genes to extract
#' @param returnValues Whether to return the numeric value associated with the top selected genes
#' @return Returns a list of key genes.
#' @export
#' @examples
#' set.seed(1234)
#' n <- 50 ## genes, rows
#' p <- 100 ## cells, cols
#' exprsMat <- matrix(rpois(n * p, lambda = 5), nrow = n)
#' rownames(exprsMat) <- paste0('gene', 1:n)
#' colnames(exprsMat) <- paste0('cell', 1:p)
#' cellTypes <- sample(letters[1:3], size = p, replace = TRUE)
#' cepo_output <- Cepo(exprsMat = exprsMat, cellTypes = cellTypes)
#' cepo_output
#' topGenes(cepo_output, n = 2)
#' topGenes(cepo_output, n = 2, returnValues = TRUE)
topGenes <- function(object, n = 5, returnValues = FALSE) {
    geneNames <- rownames(object$stats)
    
    stopifnot(n <= nrow(object$stats))
    
    if (returnValues) {
        result <- lapply(object$stats, function(this_column) {
            this_column[order(this_column, decreasing = TRUE)[seq_len(n)]]
        })
    } else {
        result <- lapply(object$stats, function(this_column) {
            geneNames[order(this_column, decreasing = TRUE)[seq_len(n)]]
        })
    }
    
    return(result)
}