Add estimateSimpleParams function

R/SimpleParams-methods.R

@@ -32,7 +32,7 @@ setMethod("show", "SimpleParams", function(object) {
 
     pp <- list("Mean:"   = c("(Rate)"       = "mean.rate",
                              "(Shape)"      = "mean.shape"),
-               "Counts:" = c("(Dispersion)" = "count.disp"))
+               "Counts:" = c("[Dispersion]" = "count.disp"))
 
     callNextMethod()
     showPP(object, pp)

R/simple-estimate.R

+estimateSimpleParams <- function(data, params = newSimpleParams()) {
+    UseMethod("estimateSimpleParams")
+}
+
+#' @rdname simpleEstimate
+#' @export
+estimateSimpleParams.SCESet <- function(data, params = newSimpleParams()) {
+    counts <- scater::counts(x)
+    estimateSimpleParams(counts, params)
+}
+
+#' @rdname simpleEstimate
+#' @importFrom stats median
+#' @export
+estimateSimpleParams.matrix <- function(data, params = newSimpleParams()) {
+
+    checkmate::assertClass(params, "SimpleParams")
+
+    # Normalise for library size and remove all zero genes
+    lib.sizes <- colSums(data)
+    lib.med <- median(lib.sizes)
+    norm.counts <- t(t(data) / lib.sizes * lib.med)
+    norm.counts <- norm.counts[rowSums(norm.counts > 0) > 1, ]
+
+    means <- rowMeans(norm.counts)
+
+    means.fit <- fitdistrplus::fitdist(means, "gamma", method = "mme")
+
+    params <- setParams(params, nGenes = nrow(data), nCells = nrow(data),
+                        mean.shape = unname(means.fit$estimate["shape"]),
+                        mean.rate = unname(means.fit$estimate["rate"]))
+
+    return(params)
+}
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