Document simLun

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.5.3
+Version: 0.5.4
 Date: 2016-10-12
 Author: Luke Zappia
 Authors@R: as.person(c(

NAMESPACE

@@ -4,11 +4,13 @@ S3method(estimateParams,SCESet)
 S3method(estimateParams,matrix)
 S3method(print,splatParams)
 export(checkParams)
+export(defaultLunParams)
 export(defaultParams)
 export(estimateParams)
 export(getParams)
 export(mergeParams)
 export(setParams)
+export(simLun)
 export(simSimple)
 export(splat)
 export(splatGroups)

R/params.R

@@ -90,6 +90,9 @@
 #' dataset by Splatter. This is also shown when a splatParams object is printed
 #' with parameters labelled as either (estimatable) or [not estimatable].
 #'
+#' Some simulations (those reproduced from publications) require additional
+#' parameters. These are described in the help for each simulation function.
+#'
 #' @return List based S3 splatParams object
 #' @examples
 #' params <- splatParams()

R/simulate-lun.R

+#' Lun simulation
+#'
+#' Simulate single-cell RNA-seq count data using the method described in Lun,
+#' Bach and Marioni "Pooling across cells to normalize single-cell RNA
+#' sequencing data with many zero counts".
+#'
+#' @param params splatParams object containing Lun simulation parameters.
+#' @param verbose logical. Whether to print progress messages.
+#' @param ... any additional parameter settings to override what is provided in
+#'        \code{params}.
+#'
+#' @details
+#' The Lun simulation generates gene mean expression levels 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}. In addition each cell is
+#' given a size factor (\code{2 ^ rnorm(nCells, mean = 0, sd = 0.5)}) and
+#' differential expression can be simulated with fixed fold changes.
+#'
+#' \code{lunSim} requires the following parameters:
+#' \itemize{
+#'   \item Common (see \code{\link{splatParams}})
+#'     \itemize{
+#'       \item nGenes
+#'       \item nCells
+#'       \item nGroups
+#'       \item groupCells
+#'       \item mean.shape
+#'       \item mean.rate
+#'       \item bcv.common
+#'       \item de.prob
+#'       \item de.downprob
+#'     }
+#'   \item Specific
+#'     \itemize{
+#'       \item [lun.upFC] - Fold change for up-regulated genes.
+#'       \item [lun.downFC] - Fold change for down-regulated genes.
+#'     }
+#' }
+#'
+#' See \code{\link{defaultLunParams}} for example of these parameters.
+#' Parameters are set in the tiered manner described in \code{\link{splat}}.
+#'
+#'
+#'
+#' @return SCESet object containing the simulated counts and intermediate values
+#'
+#' @references
+#' Lun ATL, Bach K, Marioni JC. Pooling across cells to normalize single-cell
+#' RNA sequencing data with many zero counts. Genome Biology (2016)
+#'
+#' Paper: \url{dx.doi.org/10.1186/s13059-016-0947-7}
+#'
+#' Code: \url{https://github.com/MarioniLab/Deconvolution2016}
+#'
+#' @examples
+#' sim <- simLun()
+#'
+#' @importFrom Biobase fData fData<- pData pData<- assayData
+#' @importFrom scater newSCESet
+#' @importFrom stats rnorm rgamma rnbinom
+#' @export
 simLun <- function(params = defaultLunParams(), verbose = TRUE, ...) {
 
     if (verbose) {message("Getting parameters...")}

man/defaultLunParams.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/params.R
+\name{defaultLunParams}
+\alias{defaultLunParams}
+\title{Get default Lun simulation parameters}
+\usage{
+defaultLunParams()
+}
+\value{
+A splatParams object containing default Lun parameters.
+}
+\description{
+Get a splatParams object with a set of default parameters for the Lun
+simulation.
+}
+\examples{
+params <- defaultLunParams()
+params
+}
+

man/expandParams.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/params.R
 \name{expandParams}
 \alias{expandParams}
-\title{Expath parameters}
+\title{Expand parameters}
 \usage{
 expandParams(params)
 }

man/simLun.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/simulate-lun.R
+\name{simLun}
+\alias{simLun}
+\title{Lun simulation}
+\usage{
+simLun(params = defaultLunParams(), verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{splatParams object containing Lun 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 object containing the simulated counts and intermediate values
+}
+\description{
+Simulate single-cell RNA-seq count data using the method described in Lun,
+Bach and Marioni "Pooling across cells to normalize single-cell RNA
+sequencing data with many zero counts".
+}
+\details{
+The Lun simulation generates gene mean expression levels 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}. In addition each cell is
+given a size factor (\code{2 ^ rnorm(nCells, mean = 0, sd = 0.5)}) and
+differential expression can be simulated with fixed fold changes.
+
+\code{lunSim} requires the following parameters:
+\itemize{
+  \item Common (see \code{\link{splatParams}})
+    \itemize{
+      \item nGenes
+      \item nCells
+      \item nGroups
+      \item groupCells
+      \item mean.shape
+      \item mean.rate
+      \item bcv.common
+      \item de.prob
+      \item de.downprob
+    }
+  \item Specific
+    \itemize{
+      \item [lun.upFC] - Fold change for up-regulated genes.
+      \item [lun.downFC] - Fold change for down-regulated genes.
+    }
+}
+
+See \code{\link{defaultLunParams}} for example of these parameters.
+Parameters are set in the tiered manner described in \code{\link{splat}}.
+}
+\examples{
+sim <- simLun()
+
+}
+\references{
+Lun ATL, Bach K, Marioni JC. Pooling across cells to normalize single-cell
+RNA sequencing data with many zero counts. Genome Biology (2016)
+
+Paper: \url{dx.doi.org/10.1186/s13059-016-0947-7}
+
+Code: \url{https://github.com/MarioniLab/Deconvolution2016}
+}
+

man/splatParams.Rd

@@ -100,6 +100,9 @@ parameters. It has the following sections and values:
 Those shown in brackets cannot currently be easily estimated from a real
 dataset by Splatter. This is also shown when a splatParams object is printed
 with parameters labelled as either (estimatable) or [not estimatable].
+
+Some simulations (those reproduced from publications) require additional
+parameters. These are described in the help for each simulation function.
 }
 \examples{
 params <- splatParams()