Add simSimple function

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.4.0
+Version: 0.4.1
 Date: 2016-10-12
 Author: Luke Zappia
 Authors@R: as.person(c(

NAMESPACE

@@ -9,6 +9,7 @@ export(estimateParams)
 export(getParams)
 export(mergeParams)
 export(setParams)
+export(simSimple)
 export(splat)
 export(splatGroups)
 export(splatParams)

R/simulate-simple.R

+#' 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
+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

man/bridge.Rd

 % 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}

man/getLNormFactors.Rd

 % 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}

man/getPathOrder.Rd

 % 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}

man/simBCVMeans.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simBCVMeans}
 \alias{simBCVMeans}
 \title{Simulate BCV means}

man/simDropout.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simDropout}
 \alias{simDropout}
 \title{Simulate dropout}

man/simGeneMeans.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simGeneMeans}
 \alias{simGeneMeans}
 \title{Simulate gene means}

man/simGroupCellMeans.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simGroupCellMeans}
 \alias{simGroupCellMeans}
 \title{Simulate group cell means}

man/simGroupDE.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simGroupDE}
 \alias{simGroupDE}
 \title{Simulate group differential expression}

man/simLibSizes.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simLibSizes}
 \alias{simLibSizes}
 \title{Simulate library sizes}

man/simPathCellMeans.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simPathCellMeans}
 \alias{simPathCellMeans}
 \title{Simulate path cell means}

man/simPathDE.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simPathDE}
 \alias{simPathDE}
 \title{Simulate path differential expression}

man/simSimple.Rd

+% 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()
+}
+

man/simSingleCellMeans.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simSingleCellMeans}
 \alias{simSingleCellMeans}
 \title{Simulate single population cell means}

man/simTrueCounts.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.R
+% Please edit documentation in R/simulate-splat.R
 \name{simTrueCounts}
 \alias{simTrueCounts}
 \title{Simulate true counts}

man/splat.Rd

 % 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}