Add simulateDE function

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.3.3
+Version: 0.3.4
 Date: 2016-10-09
 Author: Luke Zappia
 Authors@R: as.person(c(

R/simulate.R

@@ -70,6 +70,7 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
     pData(sim)$Group <- group.names[groups]
 
     sim <- simulateGeneMeans(sim, params)
+    sim <- simulateDE(sim, params)
 
     # Create new SCESet to make sure values are calculated correctly
     sce <- newSCESet(countData = counts(sim),
@@ -104,6 +105,27 @@ simulateGeneMeans <- function(sim, params) {
     return(sim)
 }
 
+simulateDE <- function(sim, params) {
+
+    n.genes <- getParams(params, "nGenes")
+    de.prob <- getParams(params, "de.prob")
+    de.downProb <- getParams(params, "de.downProb")
+    de.facLoc <- getParams(params, "de.facLoc")
+    de.facScale <- getParams(params, "de.facScale")
+    means.gene <- fData(sim)$GeneMean
+    group.names <- unique(pData(sim)$Group)
+
+    for (group.name in group.names) {
+        de.facs <- getLNormFactors(n.genes, de.prob, de.downProb, de.facLoc,
+                                   de.facScale)
+        group.means.gene <- means.gene * de.facs
+        fData(sim)[[paste0("DEFac", group.name)]] <- de.facs
+        fData(sim)[[paste0("GeneMean", group.name)]] <- group.means.gene
+    }
+
+    return(sim)
+}
+
 #' Get log-normal factors
 #'
 #' Randomly generate multiplication factors from a log-normal distribution.