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Commit fdbec632 authored by Luke Zappia's avatar Luke Zappia
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Add progress messages

parent 83837f38
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Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
Version: 0.3.19
Version: 0.3.20
Date: 2016-10-11
Author: Luke Zappia
Authors@R: as.person(c(
......
......@@ -111,6 +111,7 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
method <- match.arg(method)
if (verbose) {message("Getting parameters...")}
params <- setParams(params, ...)
params <- mergeParams(params, defaultParams())
params <- expandPathParams(params)
......@@ -125,6 +126,7 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
nGroups <- getParams(params, "nGroups")
group.cells <- getParams(params, "groupCells")
if (verbose) {message("Creating simulation object...")}
# Set up name vectors
cell.names <- paste0("Cell", 1:nCells)
gene.names <- paste0("Gene", 1:nGenes)
......@@ -152,19 +154,29 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
groups <- unlist(groups)
pData(sim)$Group <- group.names[groups]
if (verbose) {message("Simulating library sizes...")}
sim <- simLibSizes(sim, params)
if (verbose) {message("Simulating gene means...")}
sim <- simGeneMeans(sim, params)
if (method == "groups") {
if (verbose) {message("Simulating group DE...")}
sim <- simGroupDE(sim, params)
if (verbose) {message("Simulating cell means...")}
sim <- simGroupCellMeans(sim, params)
} else {
if (verbose) {message("Simulating path endpoints...")}
sim <- simPathDE(sim, params)
if (verbose) {message("Simulating path steps...")}
sim <- simPathCellMeans(sim, params)
}
if (verbose) {message("Simulating BCV...")}
sim <- simBCVMeans(sim, params)
if (verbose) {message("Simulating counts..")}
sim <- simTrueCounts(sim, params)
if (verbose) {message("Simulating dropout...")}
sim <- simDropout(sim, params)
if (verbose) {message("Creating final SCESet...")}
# Create new SCESet to make sure values are calculated correctly
sce <- newSCESet(countData = counts(sim),
phenoData = new("AnnotatedDataFrame", data = pData(sim)),
......@@ -177,6 +189,7 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
}
}
if (verbose) {message("Done!")}
return(sce)
}
......
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