Add initial draft of simulation code

code/simulation.R

+# Need to use real data to estimate parameters.
+# de.prob = 0.1 is the default.
+params <- newSplatParams(group.prob = rep(0.2, 5))
+sim <- splatSimulate(params, method = "groups")
+sim
+
+extract_de_inds <- function(sce) {
+  stopifnot(is(sce, "SingleCellExperiment"))
+
+  n_groups <- length(unique(colData(sce)$Group))
+  col_names <- paste0("DEFacGroup", 1:n_groups)
+  data <- rowData(sce)[, col_names]
+
+  out <- lapply(data, function(x) which(x != 1))
+
+  names(out) <- paste0("group_", 1:n_groups)
+  out
+}
+
+out <- extract_de_inds(sim)
+str(out)
+
+
+clusters <- quickCluster(sim)
+sim <- computeSumFactors(sim, clusters = clusters)
+sim <- logNormCounts(sim)
+scran_markers <- findMarkers(sim)
+
+