diff --git a/DESCRIPTION b/DESCRIPTION
index 973d0e207a9432f9afe2f21915c97817f3f7bd1b..f65f9dcf6072e31f39245743b0749bd9443e0f80 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.4.0
+Version: 0.5.0
Date: 2016-10-12
Author: Luke Zappia
Authors@R: as.person(c(
diff --git a/NAMESPACE b/NAMESPACE
index dab88fd2704d2b80f55691bcdde8c410e9e9c436..282ee47e95ec7074a8d83ee5bc61a686979eaa67 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,6 +9,7 @@ export(estimateParams)
export(getParams)
export(mergeParams)
export(setParams)
+export(simSimple)
export(splat)
export(splatGroups)
export(splatParams)
@@ -29,6 +30,7 @@ importFrom(stats,rbinom)
importFrom(stats,rchisq)
importFrom(stats,rgamma)
importFrom(stats,rlnorm)
+importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
diff --git a/NEWS.md b/NEWS.md
index 27f84e5282ea88715ea880b32e02cafaae7632bf..95a377e70f3e80f02eeb9ebb0d7eae4a256deb1c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# splatter 0.5.0
+
+* Add simple simulation
+
# splatter 0.4.0
* Add splatter simulations
diff --git a/R/simulate-simple.R b/R/simulate-simple.R
new file mode 100644
index 0000000000000000000000000000000000000000..0ab0704df4814a1a6c4df7b1be9a01a5f5e0c67e
--- /dev/null
+++ b/R/simulate-simple.R
@@ -0,0 +1,68 @@
+#' Simple simulation
+#'
+#' Simulate counts from a simple negative binomial distribution without
+#' simulated library sizes, differential expression etc.
+#'
+#' @param params splatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#' @param ... any additional parameter settings to override what is provided in
+#' \code{params}.
+#'
+#' @details
+#' Uses the following parameters: \code{nCells}, \code{nGenes},
+#' \code{mean.shape}, \code{mean.rate}, \code{bcv.common}.
+#'
+#' Gene means are simulated from a gamma distribution with
+#' \code{shape = mean.shape} and \code{rate = mean.rate}. Counts are then
+#' simulated from a negative binomial distribution with \code{mu = means} and
+#' \code{size = 1 / bcv.common}.
+#'
+#' Parameters are set in the tiered manner described in \code{\link{splat}}.
+#'
+#' @return SCESet containing simulated counts
+#' @examples
+#' sim <- simSimple()
+#' @export
+#' @importFrom stats rgamma rnbinom
+simSimple <- function(params = defaultParams(), verbose = TRUE, ...) {
+
+ if (verbose) {message("Getting parameters...")}
+ params <- setParams(params, ...)
+ params <- mergeParams(params, defaultParams())
+ params <- expandParams(params)
+
+ # Set random seed
+ seed <- getParams(params, "seed")
+ set.seed(seed)
+
+ # Get the parameters we are going to use
+ nCells <- getParams(params, "nCells")
+ nGenes <- getParams(params, "nGenes")
+ mean.shape <- getParams(params, "mean.shape")
+ mean.rate <- getParams(params, "mean.rate")
+ bcv.common <- getParams(params, "bcv.common")
+
+ if (verbose) {message("Simulating means...")}
+ means <- rgamma(nGenes, shape = mean.shape, rate = mean.rate)
+
+ if (verbose) {message("Simulating counts...")}
+ counts <- matrix(rnbinom(nGenes * nCells, mu = means,
+ size = 1 / bcv.common),
+ nrow = nGenes, ncol = nCells)
+
+ if (verbose) {message("Creating final SCESet...")}
+ cell.names <- paste0("Cell", 1:nCells)
+ gene.names <- paste0("Gene", 1:nGenes)
+
+ rownames(counts) <- gene.names
+ colnames(counts) <- cell.names
+ phenos <- new("AnnotatedDataFrame", data = data.frame(Cell = cell.names))
+ rownames(phenos) <- cell.names
+ features <- new("AnnotatedDataFrame",
+ data = data.frame(Gene = gene.names, GeneMean = means))
+ rownames(features) <- gene.names
+ sim <- newSCESet(countData = counts, phenoData = phenos,
+ featureData = features)
+
+ return(sim)
+}
\ No newline at end of file
diff --git a/R/simulate.R b/R/simulate-splat.R
similarity index 95%
rename from R/simulate.R
rename to R/simulate-splat.R
index 2b963040197ac80492f4e45aaee09946263e8aad..40b42c6c87a13631288a9a340ff0b7cf7e1b707f 100644
--- a/R/simulate.R
+++ b/R/simulate-splat.R
@@ -92,6 +92,14 @@
#' \code{underscore_naming}.
#'
#' @return SCESet object containing the simulated counts and intermediate values
+#'
+#' @seealso
+#' \code{\link{addLibSizes}}, \code{\link{addGeneMeans}},
+#' \code{\link{addSingleCellMeans}}, \code{\link{addGroupDE}},
+#' \code{\link{addGroupCellMeans}}, \code{\link{addPathDE}},
+#' \code{\link{addPathCellMeans}}, \code{\link{addBCVMeans}},
+#' \code{\link{addTrueCounts}}, \code{\link{addDropout}}
+#'
#' @examples
#' # Simulation with default parameters
#' sim <- splat()
@@ -164,28 +172,28 @@ splat <- function(params = defaultParams(),
}
if (verbose) {message("Simulating library sizes...")}
- sim <- simLibSizes(sim, params)
+ sim <- addLibSizes(sim, params)
if (verbose) {message("Simulating gene means...")}
- sim <- simGeneMeans(sim, params)
+ sim <- addGeneMeans(sim, params)
if (method == "single") {
- sim <- simSingleCellMeans(sim, params)
+ sim <- addSingleCellMeans(sim, params)
} else if (method == "groups") {
if (verbose) {message("Simulating group DE...")}
- sim <- simGroupDE(sim, params)
+ sim <- addGroupDE(sim, params)
if (verbose) {message("Simulating cell means...")}
- sim <- simGroupCellMeans(sim, params)
+ sim <- addGroupCellMeans(sim, params)
} else {
if (verbose) {message("Simulating path endpoints...")}
- sim <- simPathDE(sim, params)
+ sim <- addPathDE(sim, params)
if (verbose) {message("Simulating path steps...")}
- sim <- simPathCellMeans(sim, params)
+ sim <- addPathCellMeans(sim, params)
}
if (verbose) {message("Simulating BCV...")}
- sim <- simBCVMeans(sim, params)
+ sim <- addBCVMeans(sim, params)
if (verbose) {message("Simulating counts..")}
- sim <- simTrueCounts(sim, params)
+ sim <- addTrueCounts(sim, params)
if (verbose) {message("Simulating dropout...")}
- sim <- simDropout(sim, params)
+ sim <- addDropout(sim, params)
if (verbose) {message("Creating final SCESet...")}
# Create new SCESet to make sure values are calculated correctly
@@ -236,7 +244,7 @@ splatPaths <- function(params = defaultParams(), verbose = TRUE, ...) {
#'
#' @importFrom Biobase pData pData<-
#' @importFrom stats rlnorm
-simLibSizes <- function(sim, params) {
+addLibSizes <- function(sim, params) {
nCells <- getParams(params, "nCells")
lib.loc <- getParams(params, "lib.loc")
@@ -261,7 +269,7 @@ simLibSizes <- function(sim, params) {
#'
#' @importFrom Biobase fData fData<-
#' @importFrom stats rgamma median
-simGeneMeans <- function(sim, params) {
+addGeneMeans <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
mean.shape <- getParams(params, "mean.shape")
@@ -302,7 +310,7 @@ simGeneMeans <- function(sim, params) {
#' @return SCESet with added differential expression.
#'
#' @importFrom Biobase fData
-simGroupDE <- function(sim, params) {
+addGroupDE <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nGroups <- getParams(params, "nGroups")
@@ -326,7 +334,7 @@ simGroupDE <- function(sim, params) {
#' Simulate path differential expression
#'
#' Simulate differential expression for path. Similar to
-#' \code{\link{simGroupDE}} but care has to be taken to make sure paths are
+#' \code{\link{addGroupDE}} but care has to be taken to make sure paths are
#' processed in the correct order.
#'
#' @param sim SCESet to add differential expression to.
@@ -335,7 +343,7 @@ simGroupDE <- function(sim, params) {
#' @return SCESet with added differential expression.
#'
#' @importFrom Biobase fData
-simPathDE <- function(sim, params) {
+addPathDE <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
de.prob <- getParams(params, "de.prob")
@@ -373,7 +381,7 @@ simPathDE <- function(sim, params) {
#' @return SCESet with added cell means.
#'
#' @importFrom Biobase fData pData assayData assayData<-
-simSingleCellMeans <- function(sim, params) {
+addSingleCellMeans <- function(sim, params) {
nCells <- getParams(params, "nCells")
cell.names <- pData(sim)$Cell
@@ -403,7 +411,7 @@ simSingleCellMeans <- function(sim, params) {
#' @return SCESet with added cell means.
#'
#' @importFrom Biobase fData pData assayData assayData<-
-simGroupCellMeans <- function(sim, params) {
+addGroupCellMeans <- function(sim, params) {
nGroups <- getParams(params, "nGroups")
cell.names <- pData(sim)$Cell
@@ -438,7 +446,7 @@ simGroupCellMeans <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData
#' @importFrom stats rbinom
-simPathCellMeans <- function(sim, params) {
+addPathCellMeans <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nGroups <- getParams(params, "nGroups")
@@ -523,7 +531,7 @@ simPathCellMeans <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData assayData<-
#' @importFrom stats rchisq rgamma
-simBCVMeans <- function(sim, params) {
+addBCVMeans <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nCells <- getParams(params, "nCells")
@@ -564,7 +572,7 @@ simBCVMeans <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData
#' @importFrom stats rpois
-simTrueCounts <- function(sim, params) {
+addTrueCounts <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nCells <- getParams(params, "nCells")
@@ -597,7 +605,7 @@ simTrueCounts <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData assayData<-
#' @importFrom stats rbinom
-simDropout <- function(sim, params) {
+addDropout <- function(sim, params) {
dropout.present <- getParams(params, "dropout.present")
true.counts <- assayData(sim)$TrueCounts
diff --git a/man/simBCVMeans.Rd b/man/addBCVMeans.Rd
similarity index 79%
rename from man/simBCVMeans.Rd
rename to man/addBCVMeans.Rd
index 805c6310087ef20dbb89cc51229bb28f2deade4a..c0415b1c8de1d7f769fe598f051907ccf6f02dce 100644
--- a/man/simBCVMeans.Rd
+++ b/man/addBCVMeans.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simBCVMeans}
-\alias{simBCVMeans}
+% Please edit documentation in R/simulate-splat.R
+\name{addBCVMeans}
+\alias{addBCVMeans}
\title{Simulate BCV means}
\usage{
-simBCVMeans(sim, params)
+addBCVMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add BCV means to.}
diff --git a/man/simDropout.Rd b/man/addDropout.Rd
similarity index 82%
rename from man/simDropout.Rd
rename to man/addDropout.Rd
index fa424797af3e71e77312ea854fb31d721337e133..f8f95410d0919a17d732f0bba63adc4c86085eb1 100644
--- a/man/simDropout.Rd
+++ b/man/addDropout.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simDropout}
-\alias{simDropout}
+% Please edit documentation in R/simulate-splat.R
+\name{addDropout}
+\alias{addDropout}
\title{Simulate dropout}
\usage{
-simDropout(sim, params)
+addDropout(sim, params)
}
\arguments{
\item{sim}{SCESet to add dropout to.}
diff --git a/man/simGeneMeans.Rd b/man/addGeneMeans.Rd
similarity index 80%
rename from man/simGeneMeans.Rd
rename to man/addGeneMeans.Rd
index 6d6736e1352c0724035a663c7e5e9e8826375c8c..2419b716476d4088c81e774ac6c80d432ed64c56 100644
--- a/man/simGeneMeans.Rd
+++ b/man/addGeneMeans.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simGeneMeans}
-\alias{simGeneMeans}
+% Please edit documentation in R/simulate-splat.R
+\name{addGeneMeans}
+\alias{addGeneMeans}
\title{Simulate gene means}
\usage{
-simGeneMeans(sim, params)
+addGeneMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add gene means to.}
diff --git a/man/simGroupCellMeans.Rd b/man/addGroupCellMeans.Rd
similarity index 78%
rename from man/simGroupCellMeans.Rd
rename to man/addGroupCellMeans.Rd
index 8bc7c65718cbce8d109461982a22d7be779fc418..9c147dfc117805dc29fd57129eb7863f123233fa 100644
--- a/man/simGroupCellMeans.Rd
+++ b/man/addGroupCellMeans.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simGroupCellMeans}
-\alias{simGroupCellMeans}
+% Please edit documentation in R/simulate-splat.R
+\name{addGroupCellMeans}
+\alias{addGroupCellMeans}
\title{Simulate group cell means}
\usage{
-simGroupCellMeans(sim, params)
+addGroupCellMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add cell means to.}
diff --git a/man/simGroupDE.Rd b/man/addGroupDE.Rd
similarity index 81%
rename from man/simGroupDE.Rd
rename to man/addGroupDE.Rd
index 6a0c7c710086b6cdc6790eed4d11917b9eaadd36..c941b7268772b8672c0dcc3b66245390aec56ad5 100644
--- a/man/simGroupDE.Rd
+++ b/man/addGroupDE.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simGroupDE}
-\alias{simGroupDE}
+% Please edit documentation in R/simulate-splat.R
+\name{addGroupDE}
+\alias{addGroupDE}
\title{Simulate group differential expression}
\usage{
-simGroupDE(sim, params)
+addGroupDE(sim, params)
}
\arguments{
\item{sim}{SCESet to add differential expression to.}
diff --git a/man/simLibSizes.Rd b/man/addLibSizes.Rd
similarity index 74%
rename from man/simLibSizes.Rd
rename to man/addLibSizes.Rd
index 33b1babbe58597e1b97bb87719f7368fa588405c..bec92dfb96a221a0ccf1a089ef151edc4bf5d8ff 100644
--- a/man/simLibSizes.Rd
+++ b/man/addLibSizes.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simLibSizes}
-\alias{simLibSizes}
+% Please edit documentation in R/simulate-splat.R
+\name{addLibSizes}
+\alias{addLibSizes}
\title{Simulate library sizes}
\usage{
-simLibSizes(sim, params)
+addLibSizes(sim, params)
}
\arguments{
\item{sim}{SCESet to add library size to.}
diff --git a/man/simPathCellMeans.Rd b/man/addPathCellMeans.Rd
similarity index 79%
rename from man/simPathCellMeans.Rd
rename to man/addPathCellMeans.Rd
index 2f932198f21dde760fe5180621cb63a3c512905b..a382283cda37fbe38f3b1f4d3c1619aca3297109 100644
--- a/man/simPathCellMeans.Rd
+++ b/man/addPathCellMeans.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simPathCellMeans}
-\alias{simPathCellMeans}
+% Please edit documentation in R/simulate-splat.R
+\name{addPathCellMeans}
+\alias{addPathCellMeans}
\title{Simulate path cell means}
\usage{
-simPathCellMeans(sim, params)
+addPathCellMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add cell means to.}
diff --git a/man/simPathDE.Rd b/man/addPathDE.Rd
similarity index 69%
rename from man/simPathDE.Rd
rename to man/addPathDE.Rd
index 724ce32e67f725c125f96d11d6f042dc74f18877..2846ab15b4b1f0663a3d5d5fcf4895ef607eb6a5 100644
--- a/man/simPathDE.Rd
+++ b/man/addPathDE.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simPathDE}
-\alias{simPathDE}
+% Please edit documentation in R/simulate-splat.R
+\name{addPathDE}
+\alias{addPathDE}
\title{Simulate path differential expression}
\usage{
-simPathDE(sim, params)
+addPathDE(sim, params)
}
\arguments{
\item{sim}{SCESet to add differential expression to.}
@@ -16,7 +16,7 @@ SCESet with added differential expression.
}
\description{
Simulate differential expression for path. Similar to
-\code{\link{simGroupDE}} but care has to be taken to make sure paths are
+\code{\link{addGroupDE}} but care has to be taken to make sure paths are
processed in the correct order.
}
diff --git a/man/simSingleCellMeans.Rd b/man/addSingleCellMeans.Rd
similarity index 72%
rename from man/simSingleCellMeans.Rd
rename to man/addSingleCellMeans.Rd
index 30559e63092a4509c3d7093d160853b530550823..2b410c75091796e0245ca877e28b4ef0366068d8 100644
--- a/man/simSingleCellMeans.Rd
+++ b/man/addSingleCellMeans.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simSingleCellMeans}
-\alias{simSingleCellMeans}
+% Please edit documentation in R/simulate-splat.R
+\name{addSingleCellMeans}
+\alias{addSingleCellMeans}
\title{Simulate single population cell means}
\usage{
-simSingleCellMeans(sim, params)
+addSingleCellMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add cell means to.}
diff --git a/man/simTrueCounts.Rd b/man/addTrueCounts.Rd
similarity index 79%
rename from man/simTrueCounts.Rd
rename to man/addTrueCounts.Rd
index 2b537aa8b296dda4f9a325f938dcad17f9a737a8..5bc3034b24f1d78dffe31637176a74aafd01ef8c 100644
--- a/man/simTrueCounts.Rd
+++ b/man/addTrueCounts.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
-\name{simTrueCounts}
-\alias{simTrueCounts}
+% Please edit documentation in R/simulate-splat.R
+\name{addTrueCounts}
+\alias{addTrueCounts}
\title{Simulate true counts}
\usage{
-simTrueCounts(sim, params)
+addTrueCounts(sim, params)
}
\arguments{
\item{sim}{SCESet to add true counts to.}
diff --git a/man/bridge.Rd b/man/bridge.Rd
index 4b7b8e9ee8ec3d614f542bc187df357b6ae900c9..ec1ac3c257c1a2cc8d8c579902f1505c4443fdb6 100644
--- a/man/bridge.Rd
+++ b/man/bridge.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
\name{bridge}
\alias{bridge}
\title{Brownian bridge}
diff --git a/man/getLNormFactors.Rd b/man/getLNormFactors.Rd
index 9634fa29250fea9930932f4e531a14171c47d259..43f35f8d2d95d42630238f17bcfb9567ad922bae 100644
--- a/man/getLNormFactors.Rd
+++ b/man/getLNormFactors.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
\name{getLNormFactors}
\alias{getLNormFactors}
\title{Get log-normal factors}
diff --git a/man/getPathOrder.Rd b/man/getPathOrder.Rd
index f7f7bd1ab2ed6c7d70046d2f2d9dc2af288cea2d..e57b4af5f861747a0eb7ec20a98d4d3c7d9457a0 100644
--- a/man/getPathOrder.Rd
+++ b/man/getPathOrder.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
\name{getPathOrder}
\alias{getPathOrder}
\title{Get path order}
diff --git a/man/simSimple.Rd b/man/simSimple.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..1a566122895d44fc5e7ee61ae4c4210c68210d82
--- /dev/null
+++ b/man/simSimple.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/simulate-simple.R
+\name{simSimple}
+\alias{simSimple}
+\title{Simple simulation}
+\usage{
+simSimple(params = defaultParams(), verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{splatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+
+\item{...}{any additional parameter settings to override what is provided in
+\code{params}.}
+}
+\value{
+SCESet containing simulated counts
+}
+\description{
+Simulate counts from a simple negative binomial distribution without
+simulated library sizes, differential expression etc.
+}
+\details{
+Uses the following parameters: \code{nCells}, \code{nGenes},
+\code{mean.shape}, \code{mean.rate}, \code{bcv.common}.
+
+Gene means are simulated from a gamma distribution with
+\code{shape = mean.shape} and \code{rate = mean.rate}. Counts are then
+simulated from a negative binomial distribution with \code{mu = means} and
+\code{size = 1 / bcv.common}.
+
+Parameters are set in the tiered manner described in \code{\link{splat}}.
+}
+\examples{
+sim <- simSimple()
+}
+
diff --git a/man/splat.Rd b/man/splat.Rd
index f59b99add683d9a5cb28f29c09a37a63328e8e38..461e52e9a019d5ede95693c7c0d34b6317fef992 100644
--- a/man/splat.Rd
+++ b/man/splat.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
\name{splat}
\alias{splat}
\alias{splatGroups}
@@ -117,4 +117,11 @@ sim <- splat(params, mean.rate = 0.6, out.prob = 0.2)
# Simulate paths instead of groups
sim <- splat(method = "paths")
}
+\seealso{
+\code{\link{addLibSizes}}, \code{\link{addGeneMeans}},
+\code{\link{addSingleCellMeans}}, \code{\link{addGroupDE}},
+\code{\link{addGroupCellMeans}}, \code{\link{addPathDE}},
+\code{\link{addPathCellMeans}}, \code{\link{addBCVMeans}},
+\code{\link{addTrueCounts}}, \code{\link{addDropout}}
+}
diff --git a/tests/testthat/test-simulate-simple.R b/tests/testthat/test-simulate-simple.R
new file mode 100644
index 0000000000000000000000000000000000000000..832c34d91f771e0b6fe3a8adcde5305ca2bde9fe
--- /dev/null
+++ b/tests/testthat/test-simulate-simple.R
@@ -0,0 +1,5 @@
+context("simple simulation")
+
+test_that("simple simulation output is valid", {
+ expect_true(validObject(simSimple()))
+})
diff --git a/tests/testthat/test-simulate.R b/tests/testthat/test-simulate-splat.R
similarity index 100%
rename from tests/testthat/test-simulate.R
rename to tests/testthat/test-simulate-splat.R