Address Bioconductor build warnings, notes

* Add locfit to NAMESPACE * Add return values to logistic, showPP documentation * Delete commented mergeParams function * Switch to aes_string in compareSCESets * Add examples to getParam, setParam * Adjust line lengths * Adjust indentation

Address Bioconductor build warnings, notes
9df97dd1 · Luke Zappia · 4097cba4 · 9df97dd1 · 9df97dd1 · 9df97dd1
Commit 9df97dd1 authored 8 years ago by Luke Zappia
--- a/DESCRIPTION
+++ b/DESCRIPTION
 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.99.0
+Version: 0.99.1
-Date: 2016-12-05
+Date: 2016-12-12
 Author: Luke Zappia
 Authors@R:
    c(person("Luke", "Zappia", role = c("aut", "cre"),

--- a/NAMESPACE
+++ b/NAMESPACE
@@ -53,7 +53,7 @@ importFrom(checkmate,checkIntegerish)
 importFrom(checkmate,checkLogical)
 importFrom(checkmate,checkNumber)
 importFrom(checkmate,checkNumeric)
-importFrom(ggplot2,aes)
+importFrom(ggplot2,aes_string)
 importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_smooth)
@@ -65,6 +65,7 @@ importFrom(ggplot2,scale_y_log10)
 importFrom(ggplot2,theme_minimal)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
+importFrom(locfit,locfit)
 importFrom(methods,"slot<-")
 importFrom(methods,as)
 importFrom(methods,callNextMethod)

--- a/NEWS.md
+++ b/NEWS.md
+# splatter 0.99.1
+* Address Biocondutor build warnings, notes
 # splatter 0.99.0
 * Submit to Bioconductor

--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -7,9 +7,9 @@
 #' The Params class defines the following parameters:
 #'
 #' \describe{
-#'   \item{\code{[nGenes]}}{The number of genes to simulate.}
+#'     \item{\code{[nGenes]}}{The number of genes to simulate.}
-#'   \item{\code{[nCells]}}{The number of cells to simulate.}
+#'     \item{\code{[nCells]}}{The number of cells to simulate.}
-#'   \item{\code{seed}}{Seed to use for generating random numbers.}
+#'     \item{\code{seed}}{Seed to use for generating random numbers.}
 #' }
 #'
 #' The parameters shown in brackets can be estimated from real data.
@@ -34,15 +34,15 @@ setClass("Params",
 #' The simple simulation uses the following parameters:
 #'
 #' \describe{
-#'   \item{\code{nGenes}}{The number of genes to simulate.}
+#'     \item{\code{nGenes}}{The number of genes to simulate.}
-#'   \item{\code{nCells}}{The number of cells to simulate.}
+#'     \item{\code{nCells}}{The number of cells to simulate.}
-#'   \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#'     \item{\code{[seed]}}{Seed to use for generating random numbers.}
-#'   \item{\code{mean.shape}}{The shape parameter for the mean gamma
+#'     \item{\code{mean.shape}}{The shape parameter for the mean gamma
-#'   distribution.}
+#'     distribution.}
-#'   \item{\code{mean.rate}}{The rate parameter for the mean gamma
+#'     \item{\code{mean.rate}}{The rate parameter for the mean gamma
-#'   distribution.}
+#'     distribution.}
-#'   \item{\code{[count.disp]}}{The dispersion parameter for the counts negative
+#'     \item{\code{[count.disp]}}{The dispersion parameter for the counts
-#'   binomial distribution.}
+#'     negative binomial distribution.}
 #' }
 #'
 #' The parameters not shown in brackets can be estimated from real data using
@@ -70,93 +70,97 @@ setClass("SimpleParams",
 #' The Splatter simulation requires the following parameters:
 #'
 #' \describe{
-#'   \item{\code{nGenes}}{The number of genes to simulate.}
+#'     \item{\code{nGenes}}{The number of genes to simulate.}
-#'   \item{\code{nCells}}{The number of cells to simulate.}
+#'     \item{\code{nCells}}{The number of cells to simulate.}
-#'   \item{\code{[nGroups]}}{The number of groups or paths to simulate.}
+#'     \item{\code{[nGroups]}}{The number of groups or paths to simulate.}
-#'   \item{\code{[groupCells]}}{Vector giving the number of cells in each
+#'     \item{\code{[groupCells]}}{Vector giving the number of cells in each
-#'   simulation group/path.}
+#'     simulation group/path.}
-#'   \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#'     \item{\code{[seed]}}{Seed to use for generating random numbers.}
-#'   \item{\emph{Mean parameters}}{
+#'     \item{\emph{Mean parameters}}{
-#'     \describe{
+#'         \describe{
-#'       \item{\code{mean.shape}}{Shape parameter for the mean gamma
+#'             \item{\code{mean.shape}}{Shape parameter for the mean gamma
-#'       distribution.}
+#'             distribution.}
-#'       \item{\code{mean.rate}}{Rate parameter for the mean gamma
+#'             \item{\code{mean.rate}}{Rate parameter for the mean gamma
-#'       distribution.}
+#'             distribution.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Library size parameters}}{
-#'   \item{\emph{Library size parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{lib.loc}}{Location (meanlog) parameter for the
-#'       \item{\code{lib.loc}}{Location (meanlog) parameter for the library
+#'             library size log-normal distribution.}
-#'       size log-normal distribution.}
+#'             \item{\code{lib.scale}}{Scale (sdlog) parameter for the library
-#'       \item{\code{lib.scale}}{Scale (sdlog) parameter for the library size
+#'             size log-normal distribution.}
-#'       log-normal distribution.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Expression outlier parameters}}{
-#'   \item{\emph{Expression outlier parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{out.prob}}{Probability that a gene is an expression
-#'       \item{\code{out.prob}}{Probability that a gene is an expression
+#'             outlier.}
-#'       outlier.}
+#'             \item{\code{out.loProb}}{Probability that an expression outlier
-#'       \item{\code{out.loProb}}{Probability that an expression outlier gene
+#'             gene is lowly expressed.}
-#'       is lowly expressed.}
+#'             \item{\code{out.facLoc}}{Location (meanlog) parameter for the
-#'       \item{\code{out.facLoc}}{Location (meanlog) parameter for the
+#'             expression outlier factor log-normal distribution.}
-#'       expression outlier factor log-normal distribution.}
+#'             \item{\code{out.facScale}}{Scale (sdlog) parameter for the
-#'       \item{\code{out.facScale}}{Scale (sdlog) parameter for the expression
+#'             expression outlier factor log-normal distribution.}
-#'       outlier factor log-normal distribution.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Differential expression parameters}}{
-#'   \item{\emph{Differential expression parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{[de.prob]}}{Probability that a gene is differentially
-#'       \item{\code{[de.prob]}}{Probability that a gene is differentially
+#'             expressed in a group. Can be a vector.}
-#'       expressed in a group. Can be a vector.}
+#'             \item{\code{[de.loProb]}}{Probability that a differentially
-#'       \item{\code{[de.loProb]}}{Probability that a differentially expressed
+#'             expressed gene is down-regulated. Can be a vector.}
-#'       gene is down-regulated. Can be a vector.}
+#'             \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
-#'       \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
+#'             differential expression factor log-normal distribution. Can be a
-#'       differential expression factor log-normal distribution. Can be a
+#'             vector.}
-#'       vector.}
+#'             \item{\code{[de.facScale]}}{Scale (sdlog) parameter for the
-#'       \item{\code{[de.facScale]}}{Scale (sdlog) parameter for the
+#'             differential expression factor log-normal distribution. Can be a
-#'       differential expression factor log-normal distribution. Can be a
+#'             vector.}
-#'       vector.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Biological Coefficient of Variation parameters}}{
-#'   \item{\emph{Biological Coefficient of Variation parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{bcv.common}}{Underlying common dispersion across all
-#'       \item{\code{bcv.common}}{Underlying common dispersion across all
+#'             genes.}
-#'       genes.}
+#'             \item{\code{bcv.df}}{Degrees of Freedom for the BCV inverse
-#'       \item{\code{bcv.df}}{Degrees of Freedom for the BCV inverse chi-squared
+#'             chi-squared distribution.}
-#'       distribution.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Dropout parameters}}{
-#'   \item{\emph{Dropout parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{dropout.present}}{Logical. Whether to simulate
-#'       \item{\code{dropout.present}}{Logical. Whether to simulate dropout.}
+#'             dropout.}
-#'       \item{\code{dropout.mid}}{Midpoint parameter for the dropout logistic
+#'             \item{\code{dropout.mid}}{Midpoint parameter for the dropout
-#'       function.}
+#'             logistic function.}
-#'       \item{\code{dropout.shape}}{Shape parameter for the dropout logistic
+#'             \item{\code{dropout.shape}}{Shape parameter for the dropout
-#'       function.}
+#'             logistic function.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Differentiation path parameters}}{
-#'   \item{\emph{Differentiation path parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{[path.from]}}{Vector giving the originating point of
-#'       \item{\code{[path.from]}}{Vector giving the originating point of each
+#'             each path. This allows path structure such as a cell type which
-#'       path. This allows path structure such as a cell type which
+#'             differentiates into an intermediate cell type that then
-#'       differentiates into an intermediate cell type that then differentiates
+#'             differentiates into two mature cell types. A path structure of
-#'       into two mature cell types. A path structure of this form would have a
+#'             this form would have a "from" parameter of c(0, 1, 1) (where 0 is
-#'       "from" parameter of c(0, 1, 1) (where 0 is the origin). If no vector is
+#'             the origin). If no vector is given all paths will start at the
-#'       given all paths will start at the origin.}
+#'             origin.}
-#'       \item{\code{[path.length]}}{Vector giving the number of steps to
+#'             \item{\code{[path.length]}}{Vector giving the number of steps to
-#'       simulate along each path. If a single value is given it will be applied
+#'             simulate along each path. If a single value is given it will be
-#'       to all paths.}
+#'             applied to all paths.}
-#'       \item{\code{[path.skew]}}{Vector giving the skew of each path. Values
+#'             \item{\code{[path.skew]}}{Vector giving the skew of each path.
-#'       closer to 1 will give more cells towards the starting population,
+#'             Values closer to 1 will give more cells towards the starting
-#'       values closer to 0 will give more cells towards the final population.
+#'             population, values closer to 0 will give more cells towards the
-#'       If a single value is given it will be applied to all paths.}
+#'             final population. If a single value is given it will be applied
-#'       \item{\code{[path.nonlinearProb]}}{Probability that a gene follows a
+#'             to all paths.}
-#'       non-linear path along the differentiation path. This allows more
+#'             \item{\code{[path.nonlinearProb]}}{Probability that a gene
-#'       complex gene patterns such as a gene being equally expressed at the
+#'             follows a non-linear path along the differentiation path. This
-#'       beginning an end of a path but lowly expressed in the middle.}
+#'             allows more complex gene patterns such as a gene being equally
-#'       \item{\code{[path.sigmaFac]}}{Sigma factor for non-linear gene paths.
+#'             expressed at the beginning an end of a path but lowly expressed
-#'       A higher value will result in more extreme non-linear variations along
+#'             in the middle.}
-#'       a path.}
+#'             \item{\code{[path.sigmaFac]}}{Sigma factor for non-linear gene
+#'             paths. A higher value will result in more extreme non-linear
+#'             variations along a path.}
 #'     }
 #'   }
 #' }
@@ -229,34 +233,35 @@ setClass("SplatParams",
 #' The Lun simulation uses the following parameters:
 #'
 #' \describe{
-#'   \item{\code{nGenes}}{The number of genes to simulate.}
+#'     \item{\code{nGenes}}{The number of genes to simulate.}
-#'   \item{\code{nCells}}{The number of cells to simulate.}
+#'     \item{\code{nCells}}{The number of cells to simulate.}
-#'   \item{\code{[nGroups]}}{The number of groups to simulate.}
+#'     \item{\code{[nGroups]}}{The number of groups to simulate.}
-#'   \item{\code{[groupCells]}}{Vector giving the number of cells in each
+#'     \item{\code{[groupCells]}}{Vector giving the number of cells in each
-#'   simulation group/path.}
+#'     simulation group/path.}
-#'   \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#'     \item{\code{[seed]}}{Seed to use for generating random numbers.}
-#'   \item{\emph{Mean parameters}}{
+#'     \item{\emph{Mean parameters}}{
-#'     \describe{
+#'         \describe{
-#'       \item{\code{[mean.shape]}}{Shape parameter for the mean gamma
+#'             \item{\code{[mean.shape]}}{Shape parameter for the mean gamma
-#'       distribution.}
+#'             distribution.}
-#'       \item{\code{[mean.rate]}}{Rate parameter for the mean gamma
+#'             \item{\code{[mean.rate]}}{Rate parameter for the mean gamma
-#'       distribution.}
+#'             distribution.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Counts parameters}}{
-#'   \item{\emph{Counts parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{[count.disp]}}{The dispersion parameter for the
-#'       \item{\code{[count.disp]}}{The dispersion parameter for the counts
+#'             counts negative binomial distribution.}
-#'       negative binomial distribution.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Differential expression parameters}}{
-#'   \item{\emph{Differential expression parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{[de.nGenes]}}{The number of genes that are
-#'       \item{\code{[de.nGenes]}}{The number of genes that are differentially
+#'             differentially expressed in each group}
-#'       expressed in each group}
+#'             \item{\code{[de.upProp]}}{The proportion of differentially
-#'       \item{\code{[de.upProp]}}{The proportion of differentially expressed
+#'             expressed genes that are up-regulated in each group}
-#'       genes that are up-regulated in each group}
+#'             \item{\code{[de.upFC]}}{The fold change for up-regulated genes}
-#'       \item{\code{[de.upFC]}}{The fold change for up-regulated genes}
+#'             \item{\code{[de.downFC]}}{The fold change for down-regulated
-#'       \item{\code{[de.downFC]}}{The fold change for down-regulated genes}
+#'             genes}
 #'     }
 #'   }
 #' }
@@ -290,41 +295,43 @@ setClass("LunParams",
 #' The Lun2 simulation uses the following parameters:
 #'
 #' \describe{
-#'   \item{\code{nGenes}}{The number of genes to simulate.}
+#'     \item{\code{nGenes}}{The number of genes to simulate.}
-#'   \item{\code{nCells}}{The number of cells to simulate.}
+#'     \item{\code{nCells}}{The number of cells to simulate.}
-#'   \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#'     \item{\code{[seed]}}{Seed to use for generating random numbers.}
-#'   \item{\code{[nPlates]}}{The number of plates to simulate.}
+#'     \item{\code{[nPlates]}}{The number of plates to simulate.}
-#'   \item{\emph{Plate parameters}}{
+#'     \item{\emph{Plate parameters}}{
-#'     \describe{
+#'         \describe{
-#'       \item{\code{plate.ingroup}}{Character vecotor giving the plates
+#'             \item{\code{plate.ingroup}}{Character vecotor giving the plates
-#'       considered to be part of the "ingroup".}
+#'             considered to be part of the "ingroup".}
-#'       \item{\code{plate.mod}}{Plate effect modifier factor. The plate effect
+#'             \item{\code{plate.mod}}{Plate effect modifier factor. The plate
-#'       variance is divided by this value.}
+#'             effect variance is divided by this value.}
-#'       \item{\code{plate.var}}{Plate effect variance.}
+#'             \item{\code{plate.var}}{Plate effect variance.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Gene parameters}}{
-#'   \item{\emph{Gene parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{gene.means}}{Mean expression for each gene.}
-#'       \item{\code{gene.means}}{Mean expression for each gene.}
+#'             \item{\code{gene.disps}}{Dispersion for each gene.}
-#'       \item{\code{gene.disps}}{Dispersion for each gene.}
+#'             \item{\code{gene.ziMeans}}{Zero-inflated gene means.}
-#'       \item{\code{gene.ziMeans}}{Zero-inflated gene means.}
+#'             \item{\code{gene.ziDisps}}{Zero-inflated gene dispersions.}
-#'       \item{\code{gene.ziDisps}}{Zero-inflated gene dispersions.}
+#'             \item{\code{gene.ziProps}}{Zero-inflated gene zero proportions.}
-#'       \item{\code{gene.ziProps}}{Zero-inflated gene zero proportions.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Cell parameters}}{
-#'   \item{\emph{Cell parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{cell.plates}}{Factor giving the plate that each cell
-#'       \item{\code{cell.plates}}{Factor giving the plate that each cell comes
+#'             comes from.}
-#'       from.}
+#'             \item{\code{cell.libSizes}}{Library size for each cell.}
-#'       \item{\code{cell.libSizes}}{Library size for each cell.}
+#'             \item{\code{cell.libMod}}{Modifier factor for library sizes.
-#'       \item{\code{cell.libMod}}{Modifier factor for library sizes.
+#'             The library sizes are multiplied by this value.}
-#'       The library sizes are multiplied by this value.}
+#'         }
 #'     }
-#'   }
+#'     \item{\emph{Differential expression parameters}}{
-#'   \item{\emph{Differential expression parameters}}{
+#'         \describe{
-#'     \describe{
+#'             \item{\code{de.nGenes}}{Number of differentially expressed
-#'       \item{\code{de.nGenes}}{Number of differentially expressed genes.}
+#'             genes.}
-#'       \item{\code{de.fc}}{Fold change for differentially expressed genes.}
+#'             \item{\code{de.fc}}{Fold change for differentially expressed
+#'             genes.}
 #'     }
 #'   }
 #' }
@@ -377,20 +384,20 @@ setClass("Lun2Params",
 #' The SCDD simulation uses the following parameters:
 #'
 #' \describe{
-#'   \item{\code{[nGenes]}}{The number of genes to simulate (not used).}
+#'     \item{\code{[nGenes]}}{The number of genes to simulate (not used).}
-#'   \item{\code{nCells}}{The number of cells to simulate in each condition.}
+#'     \item{\code{nCells}}{The number of cells to simulate in each condition.}
-#'   \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#'     \item{\code{[seed]}}{Seed to use for generating random numbers.}
-#'   \item{\code{SCdat}}{\code{\link{ExpressionSet}} containing real data.}
+#'     \item{\code{SCdat}}{\code{\link{ExpressionSet}} containing real data.}
-#'   \item{\code{[nDE]}}{Number of DE genes to simulate.}
+#'     \item{\code{[nDE]}}{Number of DE genes to simulate.}
-#'   \item{\code{[nDP]}}{Number of DP genes to simulate.}
+#'     \item{\code{[nDP]}}{Number of DP genes to simulate.}
-#'   \item{\code{[nDM]}}{Number of DM genes to simulate.}
+#'     \item{\code{[nDM]}}{Number of DM genes to simulate.}
-#'   \item{\code{[nDB]}}{Number of DB genes to simulate.}
+#'     \item{\code{[nDB]}}{Number of DB genes to simulate.}
-#'   \item{\code{[nEE]}}{Number of EE genes to simulate.}
+#'     \item{\code{[nEE]}}{Number of EE genes to simulate.}
-#'   \item{\code{[nEP]}}{Number of EP genes to simulate.}
+#'     \item{\code{[nEP]}}{Number of EP genes to simulate.}
-#'   \item{\code{[sd.range]}}{Interval for fold change standard deviations.}
+#'     \item{\code{[sd.range]}}{Interval for fold change standard deviations.}
-#'   \item{\code{[modeFC]}}{Values for DP, DM and DB mode fold changes.}
+#'     \item{\code{[modeFC]}}{Values for DP, DM and DB mode fold changes.}
-#'   \item{\code{[varInflation}]}{Variance inflation factors for each
+#'     \item{\code{[varInflation}]}{Variance inflation factors for each
-#'   condition.}
+#'     condition.}
 #' }
 #'
 #' The parameters not shown in brackets can be estimated from real data using

--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -22,6 +22,10 @@ NULL
 #'
 #' @return The extracted parameter value
 #'
+#' @examples
+#' params <- newSimpleParams()
+#' getParam(params, "nGenes")
+#'
 #' @rdname getParam
 #' @export
 setGeneric("getParam", function(object, name) {standardGeneric("getParam")})
@@ -36,10 +40,14 @@ setGeneric("getParam", function(object, name) {standardGeneric("getParam")})
 #'
 #' @return Object with new parameter value.
 #'
+#' @examples
+#' params <- newSimpleParams()
+#' setParam(params, "nGenes", 100)
+#'
 #' @rdname setParam
 #' @export
 setGeneric("setParam",
-           function(object, name, value) {
+          function(object, name, value) {
               standardGeneric("setParam")
 })

--- a/R/compare.R
+++ b/R/compare.R
@@ -9,19 +9,21 @@
 #' The return list has three items:
 #'
 #' \describe{
-#'   \item{\code{FeatureData}}{Combined feature data from the provided SCESets.}
+#'     \item{\code{FeatureData}}{Combined feature data from the provided
-#'   \item{\code{PhenoData}}{Combined pheno data from the provided SCESets.}
+#'     SCESets.}
-#'   \item{\code{Plots}}{Comparison plots
+#'     \item{\code{PhenoData}}{Combined pheno data from the provided SCESets.}
-#'     \describe{
+#'     \item{\code{Plots}}{Comparison plots
-#'       \item{\code{Means}}{Violin plot of mean distribution.}
+#'         \describe{
-#'       \item{\code{Variances}}{Violin plot of variance distribution.}
+#'             \item{\code{Means}}{Violin plot of mean distribution.}
-#'       \item{\code{MeanVar}}{Scatter plot with fitted lines showing the
+#'             \item{\code{Variances}}{Violin plot of variance distribution.}
-#'       mean-variance relationship.}
+#'             \item{\code{MeanVar}}{Scatter plot with fitted lines showing the
-#'       \item{\code{LibraySizes}}{Boxplot of the library size distribution.}
+#'             mean-variance relationship.}
-#'       \item{\code{ZerosGene}}{Boxplot of the percentage of each gene that is
+#'             \item{\code{LibraySizes}}{Boxplot of the library size
-#'       zero.}
+#'             distribution.}
-#'       \item{\code{ZerosCell}}{Boxplot of the percentage of each cell that is
+#'             \item{\code{ZerosGene}}{Boxplot of the percentage of each gene
-#'       zero.}
+#'             that is zero.}
+#'             \item{\code{ZerosCell}}{Boxplot of the percentage of each cell
+#'             that is zero.}
 #'     }
 #'   }
 #' }
@@ -39,7 +41,7 @@
 #' comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
 #' names(comparison)
 #' names(comparison$Plots)
-#' @importFrom ggplot2 ggplot aes geom_point geom_smooth geom_boxplot
+#' @importFrom ggplot2 ggplot aes_string geom_point geom_smooth geom_boxplot
 #' geom_violin scale_y_continuous scale_y_log10 xlab ylab ggtitle theme_minimal
 #' @importFrom scater cpm<-
 #' @export
@@ -48,7 +50,6 @@ compareSCESets <- function(sces) {
    checkmate::assertList(sces, types = "SCESet", any.missing = FALSE,
                          min.len = 1, names = "unique")
    for (name in names(sces)) {
        sce <- sces[[name]]
        fData(sce)$Dataset <- name
@@ -76,14 +77,16 @@ compareSCESets <- function(sces) {
    pData.all$Dataset <- factor(pData.all$Dataset, levels = names(sces))
    means <- ggplot(fData.all,
-                    aes(x = Dataset, y = mean_log_cpm, colour = Dataset)) +
+                    aes_string(x = "Dataset", y = "mean_log_cpm",
+                               colour = "Dataset")) +
        geom_violin(draw_quantiles = c(0.25, 0.5, 0.75)) +
        ylab(expression(paste("Mean ", log[2], "(CPM + 1)"))) +
        ggtitle("Distribution of mean expression") +
        theme_minimal()
    vars <- ggplot(fData.all,
-                   aes(x = Dataset, y = var_cpm, colour = Dataset)) +
+                   aes_string(x = "Dataset", y = "var_cpm",
+                              colour = "Dataset")) +
        geom_violin(draw_quantiles = c(0.25, 0.5, 0.75)) +
        scale_y_log10(labels = scales::comma) +
        ylab("CPM Variance") +
@@ -91,8 +94,8 @@ compareSCESets <- function(sces) {
        theme_minimal()
    mean.var <- ggplot(fData.all,
-                       aes(x = mean_log_cpm, y = var_log_cpm, colour = Dataset,
+                       aes_string(x = "mean_log_cpm", y = "var_log_cpm",
-                           fill = Dataset)) +
+                                  olour = "Dataset", fill = "Dataset")) +
        geom_point() +
        geom_smooth() +
        xlab(expression(paste("Mean ", log[2], "(CPM + 1)"))) +
@@ -101,7 +104,8 @@ compareSCESets <- function(sces) {
        theme_minimal()
    libs <- ggplot(pData.all,
-                   aes(x = Dataset, y = total_counts, colour = Dataset)) +
+                   aes_string(x = "Dataset", y = "total_counts",
+                              colour = "Dataset")) +
        geom_boxplot() +
        scale_y_continuous(labels = scales::comma) +
        ylab("Total counts per cell") +
@@ -109,7 +113,8 @@ compareSCESets <- function(sces) {
        theme_minimal()
    z.gene <- ggplot(fData.all,
-                     aes(x = Dataset, y = pct_dropout, colour = Dataset)) +
+                     aes_string(x = "Dataset", y = "pct_dropout",
+                                colour = "Dataset")) +
        geom_boxplot() +
        scale_y_continuous(limits = c(0, 100)) +
        ylab("Percentage zeros per gene") +
@@ -117,7 +122,8 @@ compareSCESets <- function(sces) {
        theme_minimal()
    z.cell <- ggplot(pData.all,
-                     aes(x = Dataset, y = pct_dropout, colour = Dataset)) +
+                     aes_string(x = "Dataset", y = "pct_dropout",
+                                colour = "Dataset")) +
        geom_boxplot() +
        scale_y_continuous(limits = c(0, 100)) +
        ylab("Percentage zeros per cell") +

--- a/R/lun2-estimate.R
+++ b/R/lun2-estimate.R
@@ -39,6 +39,7 @@ lun2Estimate.SCESet <- function(counts, plates, params = newLun2Params(),
 #' @rdname lun2Estimate
 #' @importFrom stats model.matrix
+#' @importFrom locfit locfit
 #' @export
 lun2Estimate.matrix <- function(counts, plates, params = newLun2Params(),
                                min.size = 200, verbose = TRUE) {
@@ -125,11 +126,12 @@ lun2Estimate.matrix <- function(counts, plates, params = newLun2Params(),
    collected <- lapply(seq_len(nrow(dge)), function(i) {
        if (progress) {pb$tick()}
        tryCatch({
-            out <- lme4::glmer(Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),
+            out <- lme4::glmer(
-                               data = data.frame(Counts = as.integer(counts[i, ]),
+                       Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),
-                                                 Group = groups,
+                       data = data.frame(Counts = as.integer(counts[i, ]),
-                                                 Plate = plates),
+                                         Group = groups,
-                               family = lme4::negative.binomial(1 / dge$tagwise[i]))
+                                         Plate = plates),
+                       family = lme4::negative.binomial(1 / dge$tagwise[i]))
            output <- unlist(lme4::VarCorr(out))
            return(output)
        }, error = function(err) {

--- a/R/params-functions.R
+++ b/R/params-functions.R
@@ -105,6 +105,8 @@ setParamsUnchecked <- function(params, update = NULL, ...) {
 #' @param params object to show.
 #' @param pp list specifying how the object should be displayed.
 #'
+#' @return Print params object to console
+#'
 #' @importFrom utils head
 showPP <- function(params, pp) {
@@ -131,29 +133,4 @@ showPP <- function(params, pp) {
        print(noquote(short.values), print.gap = 2)
        cat("\n")
    }
 }
\ No newline at end of file
-# mergeParams <- function(params1, params2) {
-#
-#     if (class(params1) != class(params2)) {
-#         stop("params1 and params2 must be of the same Params class")
-#     }
-#
-#     default <- new(class(params1))
-#
-#     update <- list()
-#     for (parameter in slotNames(params1)) {
-#         value1 <- getParam(params1, parameter)
-#         default.value <- getParam(default, parameter)
-#         if (value1 == default.value) {
-#             value2 <- getParam(params2, parameter)
-#             update[[parameter]] <- value2
-#         } else {
-#             update[[parameter]] <- value1
-#         }
-#     }
-#
-#     merged <- setParams(default, update)
-#
-#     return(merged)
-# }
\ No newline at end of file
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -24,14 +24,14 @@
 #'
 #' The simulation involves the following steps:
 #' \enumerate{
-#'   \item Set up simulation object
+#'     \item Set up simulation object
-#'   \item Simulate library sizes
+#'     \item Simulate library sizes
-#'   \item Simulate gene means
+#'     \item Simulate gene means
-#'   \item Simulate groups/paths
+#'     \item Simulate groups/paths
-#'   \item Simulate BCV adjusted cell means
+#'     \item Simulate BCV adjusted cell means
-#'   \item Simulate true counts
+#'     \item Simulate true counts
-#'   \item Simulate dropout
+#'     \item Simulate dropout
-#'   \item Create final SCESet object
+#'     \item Create final SCESet object
 #' }
 #'
 #' The final output is an \code{\link[scater]{SCESet}} object that contains the
@@ -41,41 +41,41 @@
 #' information) or \code{\link[Biobase]{assayData}} (for gene by cell matrices)
 #' slots. This additional information includes:
 #' \describe{
-#'   \item{\code{phenoData}}{
+#'     \item{\code{phenoData}}{
-#'     \describe{
+#'         \describe{
-#'       \item{Cell}{Unique cell identifier.}
+#'             \item{Cell}{Unique cell identifier.}
-#'       \item{Group}{The group or path the cell belongs to.}
+#'             \item{Group}{The group or path the cell belongs to.}
-#'       \item{ExpLibSize}{The expected library size for that cell.}
+#'             \item{ExpLibSize}{The expected library size for that cell.}
-#'       \item{Step (paths only)}{how far along the path each cell is.}
+#'             \item{Step (paths only)}{how far along the path each cell is.}
+#'         }
 #'     }
-#'   }
+#'     \item{\code{featureData}}{
-#'   \item{\code{featureData}}{
+#'         \describe{
-#'     \describe{
+#'             \item{Gene}{Unique gene identifier.}
-#'       \item{Gene}{Unique gene identifier.}
+#'             \item{BaseGeneMean}{The base expression level for that gene.}
-#'       \item{BaseGeneMean}{The base expression level for that gene.}
+#'             \item{OutlierFactor}{Expression outlier factor for that gene. Values
-#'       \item{OutlierFactor}{Expression outlier factor for that gene. Values
+#'             of 1 indicate the gene is not an expression outlier.}
-#'       of 1 indicate the gene is not an expression outlier.}
+#'             \item{GeneMean}{Expression level after applying outlier factors.}
-#'       \item{GeneMean}{Expression level after applying outlier factors.}
+#'             \item{DEFac[Group]}{The differential expression factor for each gene
-#'       \item{DEFac[Group]}{The differential expression factor for each gene
+#'             in a particular group. Values of 1 indicate the gene is not
-#'       in a particular group. Values of 1 indicate the gene is not
+#'             differentially expressed.}
-#'       differentially expressed.}
+#'             \item{GeneMean[Group]}{Expression level of a gene in a particular
-#'       \item{GeneMean[Group]}{Expression level of a gene in a particular
+#'             group after applying differential expression factors.}
-#'       group after applying differential expression factors.}
+#'         }
 #'     }
-#'   }
+#'     \item{\code{assayData}}{
-#'   \item{\code{assayData}}{
+#'         \describe{
-#'     \describe{
+#'             \item{BaseCellMeans}{The expression of genes in each cell adjusted for
-#'       \item{BaseCellMeans}{The expression of genes in each cell adjusted for
+#'             expected library size.}
-#'       expected library size.}
+#'             \item{BCV}{The Biological Coefficient of Variation for each gene in
-#'       \item{BCV}{The Biological Coefficient of Variation for each gene in
+#'             each cell.}
-#'       each cell.}
+#'             \item{CellMeans}{The expression level of genes in each cell adjusted
-#'       \item{CellMeans}{The expression level of genes in each cell adjusted
+#'             for BCV.}
-#'       for BCV.}
+#'             \item{TrueCounts}{The simulated counts before dropout.}
-#'       \item{TrueCounts}{The simulated counts before dropout.}
+#'             \item{Dropout}{Logical matrix showing which values have been dropped
-#'       \item{Dropout}{Logical matrix showing which values have been dropped
+#'             in which cells.}
-#'       in which cells.}
+#'         }
 #'     }
-#'   }
 #' }
 #'
 #' Values that have been added by Splatter are named using \code{CamelCase} in

--- a/R/utils.R
+++ b/R/utils.R
@@ -5,6 +5,8 @@
 #' @param x value to apply the function to.
 #' @param x0 midpoint parameter. Gives the centre of the function.
 #' @param k shape parameter. Gives the slope of the function.
+#'
+#' @return Value of logistic funciton with given parameters
 logistic <- function(x, x0, k) {
    1 / (1 + exp(-k * (x - x0)))
 }

--- a/man/Lun2Params.Rd
+++ b/man/Lun2Params.Rd
@@ -14,41 +14,43 @@ S4 class that holds parameters for the Lun simulation.
 The Lun2 simulation uses the following parameters:
 \describe{
-  \item{\code{nGenes}}{The number of genes to simulate.}
+    \item{\code{nGenes}}{The number of genes to simulate.}
-  \item{\code{nCells}}{The number of cells to simulate.}
+    \item{\code{nCells}}{The number of cells to simulate.}
-  \item{\code{[seed]}}{Seed to use for generating random numbers.}
+    \item{\code{[seed]}}{Seed to use for generating random numbers.}
-  \item{\code{[nPlates]}}{The number of plates to simulate.}
+    \item{\code{[nPlates]}}{The number of plates to simulate.}
-  \item{\emph{Plate parameters}}{
+    \item{\emph{Plate parameters}}{
-    \describe{
+        \describe{
-      \item{\code{plate.ingroup}}{Character vecotor giving the plates
+            \item{\code{plate.ingroup}}{Character vecotor giving the plates
-      considered to be part of the "ingroup".}
+            considered to be part of the "ingroup".}
-      \item{\code{plate.mod}}{Plate effect modifier factor. The plate effect
+            \item{\code{plate.mod}}{Plate effect modifier factor. The plate
-      variance is divided by this value.}
+            effect variance is divided by this value.}
-      \item{\code{plate.var}}{Plate effect variance.}
+            \item{\code{plate.var}}{Plate effect variance.}
+        }
    }
-  }
+    \item{\emph{Gene parameters}}{
-  \item{\emph{Gene parameters}}{
+        \describe{
-    \describe{
+            \item{\code{gene.means}}{Mean expression for each gene.}
-      \item{\code{gene.means}}{Mean expression for each gene.}
+            \item{\code{gene.disps}}{Dispersion for each gene.}
-      \item{\code{gene.disps}}{Dispersion for each gene.}
+            \item{\code{gene.ziMeans}}{Zero-inflated gene means.}
-      \item{\code{gene.ziMeans}}{Zero-inflated gene means.}
+            \item{\code{gene.ziDisps}}{Zero-inflated gene dispersions.}
-      \item{\code{gene.ziDisps}}{Zero-inflated gene dispersions.}
+            \item{\code{gene.ziProps}}{Zero-inflated gene zero proportions.}
-      \item{\code{gene.ziProps}}{Zero-inflated gene zero proportions.}
+        }
    }
-  }
+    \item{\emph{Cell parameters}}{
-  \item{\emph{Cell parameters}}{
+        \describe{
-    \describe{
+            \item{\code{cell.plates}}{Factor giving the plate that each cell
-      \item{\code{cell.plates}}{Factor giving the plate that each cell comes
+            comes from.}
-      from.}
+            \item{\code{cell.libSizes}}{Library size for each cell.}
-      \item{\code{cell.libSizes}}{Library size for each cell.}
+            \item{\code{cell.libMod}}{Modifier factor for library sizes.
-      \item{\code{cell.libMod}}{Modifier factor for library sizes.
+            The library sizes are multiplied by this value.}
-      The library sizes are multiplied by this value.}
+        }
    }
-  }
+    \item{\emph{Differential expression parameters}}{
-  \item{\emph{Differential expression parameters}}{
+        \describe{
-    \describe{
+            \item{\code{de.nGenes}}{Number of differentially expressed
-      \item{\code{de.nGenes}}{Number of differentially expressed genes.}
+            genes.}
-      \item{\code{de.fc}}{Fold change for differentially expressed genes.}
+            \item{\code{de.fc}}{Fold change for differentially expressed
+            genes.}
    }
  }
 }

--- a/man/LunParams.Rd
+++ b/man/LunParams.Rd
@@ -14,34 +14,35 @@ S4 class that holds parameters for the Lun simulation.
 The Lun simulation uses the following parameters:
 \describe{
-  \item{\code{nGenes}}{The number of genes to simulate.}
+    \item{\code{nGenes}}{The number of genes to simulate.}
-  \item{\code{nCells}}{The number of cells to simulate.}
+    \item{\code{nCells}}{The number of cells to simulate.}
-  \item{\code{[nGroups]}}{The number of groups to simulate.}
+    \item{\code{[nGroups]}}{The number of groups to simulate.}
-  \item{\code{[groupCells]}}{Vector giving the number of cells in each
+    \item{\code{[groupCells]}}{Vector giving the number of cells in each
-  simulation group/path.}
+    simulation group/path.}
-  \item{\code{[seed]}}{Seed to use for generating random numbers.}
+    \item{\code{[seed]}}{Seed to use for generating random numbers.}
-  \item{\emph{Mean parameters}}{
+    \item{\emph{Mean parameters}}{
-    \describe{
+        \describe{
-      \item{\code{[mean.shape]}}{Shape parameter for the mean gamma
+            \item{\code{[mean.shape]}}{Shape parameter for the mean gamma
-      distribution.}
+            distribution.}
-      \item{\code{[mean.rate]}}{Rate parameter for the mean gamma
+            \item{\code{[mean.rate]}}{Rate parameter for the mean gamma
-      distribution.}
+            distribution.}
+        }
    }
-  }
+    \item{\emph{Counts parameters}}{
-  \item{\emph{Counts parameters}}{
+        \describe{
-    \describe{
+            \item{\code{[count.disp]}}{The dispersion parameter for the
-      \item{\code{[count.disp]}}{The dispersion parameter for the counts
+            counts negative binomial distribution.}
-      negative binomial distribution.}
+        }
    }
-  }
+    \item{\emph{Differential expression parameters}}{
-  \item{\emph{Differential expression parameters}}{
+        \describe{
-    \describe{
+            \item{\code{[de.nGenes]}}{The number of genes that are
-      \item{\code{[de.nGenes]}}{The number of genes that are differentially
+            differentially expressed in each group}
-      expressed in each group}
+            \item{\code{[de.upProp]}}{The proportion of differentially
-      \item{\code{[de.upProp]}}{The proportion of differentially expressed
+            expressed genes that are up-regulated in each group}
-      genes that are up-regulated in each group}
+            \item{\code{[de.upFC]}}{The fold change for up-regulated genes}
-      \item{\code{[de.upFC]}}{The fold change for up-regulated genes}
+            \item{\code{[de.downFC]}}{The fold change for down-regulated
-      \item{\code{[de.downFC]}}{The fold change for down-regulated genes}
+            genes}
    }
  }
 }

--- a/man/Params.Rd
+++ b/man/Params.Rd
@@ -14,9 +14,9 @@ Virtual S4 class that all other Params classes inherit from.
 The Params class defines the following parameters:
 \describe{
-  \item{\code{[nGenes]}}{The number of genes to simulate.}
+    \item{\code{[nGenes]}}{The number of genes to simulate.}
-  \item{\code{[nCells]}}{The number of cells to simulate.}
+    \item{\code{[nCells]}}{The number of cells to simulate.}
-  \item{\code{seed}}{Seed to use for generating random numbers.}
+    \item{\code{seed}}{Seed to use for generating random numbers.}
 }
 The parameters shown in brackets can be estimated from real data.

--- a/man/SCDDParams.Rd
+++ b/man/SCDDParams.Rd
@@ -14,20 +14,20 @@ S4 class that holds parameters for the scDD simulation.
 The SCDD simulation uses the following parameters:
 \describe{
-  \item{\code{[nGenes]}}{The number of genes to simulate (not used).}
+    \item{\code{[nGenes]}}{The number of genes to simulate (not used).}
-  \item{\code{nCells}}{The number of cells to simulate in each condition.}
+    \item{\code{nCells}}{The number of cells to simulate in each condition.}
-  \item{\code{[seed]}}{Seed to use for generating random numbers.}
+    \item{\code{[seed]}}{Seed to use for generating random numbers.}
-  \item{\code{SCdat}}{\code{\link{ExpressionSet}} containing real data.}
+    \item{\code{SCdat}}{\code{\link{ExpressionSet}} containing real data.}
-  \item{\code{[nDE]}}{Number of DE genes to simulate.}
+    \item{\code{[nDE]}}{Number of DE genes to simulate.}
-  \item{\code{[nDP]}}{Number of DP genes to simulate.}
+    \item{\code{[nDP]}}{Number of DP genes to simulate.}
-  \item{\code{[nDM]}}{Number of DM genes to simulate.}
+    \item{\code{[nDM]}}{Number of DM genes to simulate.}
-  \item{\code{[nDB]}}{Number of DB genes to simulate.}
+    \item{\code{[nDB]}}{Number of DB genes to simulate.}
-  \item{\code{[nEE]}}{Number of EE genes to simulate.}
+    \item{\code{[nEE]}}{Number of EE genes to simulate.}
-  \item{\code{[nEP]}}{Number of EP genes to simulate.}
+    \item{\code{[nEP]}}{Number of EP genes to simulate.}
-  \item{\code{[sd.range]}}{Interval for fold change standard deviations.}
+    \item{\code{[sd.range]}}{Interval for fold change standard deviations.}
-  \item{\code{[modeFC]}}{Values for DP, DM and DB mode fold changes.}
+    \item{\code{[modeFC]}}{Values for DP, DM and DB mode fold changes.}
-  \item{\code{[varInflation}]}{Variance inflation factors for each
+    \item{\code{[varInflation}]}{Variance inflation factors for each
-  condition.}
+    condition.}
 }
 The parameters not shown in brackets can be estimated from real data using

--- a/man/SimpleParams.Rd
+++ b/man/SimpleParams.Rd
@@ -14,15 +14,15 @@ S4 class that holds parameters for the simple simulation.
 The simple simulation uses the following parameters:
 \describe{
-  \item{\code{nGenes}}{The number of genes to simulate.}
+    \item{\code{nGenes}}{The number of genes to simulate.}
-  \item{\code{nCells}}{The number of cells to simulate.}
+    \item{\code{nCells}}{The number of cells to simulate.}
-  \item{\code{[seed]}}{Seed to use for generating random numbers.}
+    \item{\code{[seed]}}{Seed to use for generating random numbers.}
-  \item{\code{mean.shape}}{The shape parameter for the mean gamma
+    \item{\code{mean.shape}}{The shape parameter for the mean gamma
-  distribution.}
+    distribution.}
-  \item{\code{mean.rate}}{The rate parameter for the mean gamma
+    \item{\code{mean.rate}}{The rate parameter for the mean gamma
-  distribution.}
+    distribution.}
-  \item{\code{[count.disp]}}{The dispersion parameter for the counts negative
+    \item{\code{[count.disp]}}{The dispersion parameter for the counts
-  binomial distribution.}
+    negative binomial distribution.}
 }
 The parameters not shown in brackets can be estimated from real data using

--- a/man/SplatParams.Rd
+++ b/man/SplatParams.Rd
@@ -14,93 +14,97 @@ S4 class that holds parameters for the Splatter simulation.
 The Splatter simulation requires the following parameters:
 \describe{
-  \item{\code{nGenes}}{The number of genes to simulate.}
+    \item{\code{nGenes}}{The number of genes to simulate.}
-  \item{\code{nCells}}{The number of cells to simulate.}
+    \item{\code{nCells}}{The number of cells to simulate.}
-  \item{\code{[nGroups]}}{The number of groups or paths to simulate.}
+    \item{\code{[nGroups]}}{The number of groups or paths to simulate.}
-  \item{\code{[groupCells]}}{Vector giving the number of cells in each
+    \item{\code{[groupCells]}}{Vector giving the number of cells in each
-  simulation group/path.}
+    simulation group/path.}
-  \item{\code{[seed]}}{Seed to use for generating random numbers.}
+    \item{\code{[seed]}}{Seed to use for generating random numbers.}
-  \item{\emph{Mean parameters}}{
+    \item{\emph{Mean parameters}}{
-    \describe{
+        \describe{
-      \item{\code{mean.shape}}{Shape parameter for the mean gamma
+            \item{\code{mean.shape}}{Shape parameter for the mean gamma
-      distribution.}
+            distribution.}
-      \item{\code{mean.rate}}{Rate parameter for the mean gamma
+            \item{\code{mean.rate}}{Rate parameter for the mean gamma
-      distribution.}
+            distribution.}
+        }
    }
-  }
+    \item{\emph{Library size parameters}}{
-  \item{\emph{Library size parameters}}{
+        \describe{
-    \describe{
+            \item{\code{lib.loc}}{Location (meanlog) parameter for the
-      \item{\code{lib.loc}}{Location (meanlog) parameter for the library
+            library size log-normal distribution.}
-      size log-normal distribution.}
+            \item{\code{lib.scale}}{Scale (sdlog) parameter for the library
-      \item{\code{lib.scale}}{Scale (sdlog) parameter for the library size
+            size log-normal distribution.}
-      log-normal distribution.}
+        }
    }
-  }
+    \item{\emph{Expression outlier parameters}}{
-  \item{\emph{Expression outlier parameters}}{
+        \describe{
-    \describe{
+            \item{\code{out.prob}}{Probability that a gene is an expression
-      \item{\code{out.prob}}{Probability that a gene is an expression
+            outlier.}
-      outlier.}
+            \item{\code{out.loProb}}{Probability that an expression outlier
-      \item{\code{out.loProb}}{Probability that an expression outlier gene
+            gene is lowly expressed.}
-      is lowly expressed.}
+            \item{\code{out.facLoc}}{Location (meanlog) parameter for the
-      \item{\code{out.facLoc}}{Location (meanlog) parameter for the
+            expression outlier factor log-normal distribution.}
-      expression outlier factor log-normal distribution.}
+            \item{\code{out.facScale}}{Scale (sdlog) parameter for the
-      \item{\code{out.facScale}}{Scale (sdlog) parameter for the expression
+            expression outlier factor log-normal distribution.}
-      outlier factor log-normal distribution.}
+        }
    }
-  }
+    \item{\emph{Differential expression parameters}}{
-  \item{\emph{Differential expression parameters}}{
+        \describe{
-    \describe{
+            \item{\code{[de.prob]}}{Probability that a gene is differentially
-      \item{\code{[de.prob]}}{Probability that a gene is differentially
+            expressed in a group. Can be a vector.}
-      expressed in a group. Can be a vector.}
+            \item{\code{[de.loProb]}}{Probability that a differentially
-      \item{\code{[de.loProb]}}{Probability that a differentially expressed
+            expressed gene is down-regulated. Can be a vector.}
-      gene is down-regulated. Can be a vector.}
+            \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
-      \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
+            differential expression factor log-normal distribution. Can be a
-      differential expression factor log-normal distribution. Can be a
+            vector.}
-      vector.}
+            \item{\code{[de.facScale]}}{Scale (sdlog) parameter for the
-      \item{\code{[de.facScale]}}{Scale (sdlog) parameter for the
+            differential expression factor log-normal distribution. Can be a
-      differential expression factor log-normal distribution. Can be a
+            vector.}
-      vector.}
+        }
    }
-  }
+    \item{\emph{Biological Coefficient of Variation parameters}}{
-  \item{\emph{Biological Coefficient of Variation parameters}}{
+        \describe{
-    \describe{
+            \item{\code{bcv.common}}{Underlying common dispersion across all
-      \item{\code{bcv.common}}{Underlying common dispersion across all
+            genes.}
-      genes.}
+            \item{\code{bcv.df}}{Degrees of Freedom for the BCV inverse
-      \item{\code{bcv.df}}{Degrees of Freedom for the BCV inverse chi-squared
+            chi-squared distribution.}
-      distribution.}
+        }
    }
-  }
+    \item{\emph{Dropout parameters}}{
-  \item{\emph{Dropout parameters}}{
+        \describe{
-    \describe{
+            \item{\code{dropout.present}}{Logical. Whether to simulate
-      \item{\code{dropout.present}}{Logical. Whether to simulate dropout.}
+            dropout.}
-      \item{\code{dropout.mid}}{Midpoint parameter for the dropout logistic
+            \item{\code{dropout.mid}}{Midpoint parameter for the dropout
-      function.}
+            logistic function.}
-      \item{\code{dropout.shape}}{Shape parameter for the dropout logistic
+            \item{\code{dropout.shape}}{Shape parameter for the dropout
-      function.}
+            logistic function.}
+        }
    }
-  }
+    \item{\emph{Differentiation path parameters}}{
-  \item{\emph{Differentiation path parameters}}{
+        \describe{
-    \describe{
+            \item{\code{[path.from]}}{Vector giving the originating point of
-      \item{\code{[path.from]}}{Vector giving the originating point of each
+            each path. This allows path structure such as a cell type which
-      path. This allows path structure such as a cell type which
+            differentiates into an intermediate cell type that then
-      differentiates into an intermediate cell type that then differentiates
+            differentiates into two mature cell types. A path structure of
-      into two mature cell types. A path structure of this form would have a
+            this form would have a "from" parameter of c(0, 1, 1) (where 0 is
-      "from" parameter of c(0, 1, 1) (where 0 is the origin). If no vector is
+            the origin). If no vector is given all paths will start at the
-      given all paths will start at the origin.}
+            origin.}
-      \item{\code{[path.length]}}{Vector giving the number of steps to
+            \item{\code{[path.length]}}{Vector giving the number of steps to
-      simulate along each path. If a single value is given it will be applied
+            simulate along each path. If a single value is given it will be
-      to all paths.}
+            applied to all paths.}
-      \item{\code{[path.skew]}}{Vector giving the skew of each path. Values
+            \item{\code{[path.skew]}}{Vector giving the skew of each path.
-      closer to 1 will give more cells towards the starting population,
+            Values closer to 1 will give more cells towards the starting
-      values closer to 0 will give more cells towards the final population.
+            population, values closer to 0 will give more cells towards the
-      If a single value is given it will be applied to all paths.}
+            final population. If a single value is given it will be applied
-      \item{\code{[path.nonlinearProb]}}{Probability that a gene follows a
+            to all paths.}
-      non-linear path along the differentiation path. This allows more
+            \item{\code{[path.nonlinearProb]}}{Probability that a gene
-      complex gene patterns such as a gene being equally expressed at the
+            follows a non-linear path along the differentiation path. This
-      beginning an end of a path but lowly expressed in the middle.}
+            allows more complex gene patterns such as a gene being equally
-      \item{\code{[path.sigmaFac]}}{Sigma factor for non-linear gene paths.
+            expressed at the beginning an end of a path but lowly expressed
-      A higher value will result in more extreme non-linear variations along
+            in the middle.}
-      a path.}
+            \item{\code{[path.sigmaFac]}}{Sigma factor for non-linear gene
+            paths. A higher value will result in more extreme non-linear
+            variations along a path.}
    }
  }
 }

--- a/man/compareSCESets.Rd
+++ b/man/compareSCESets.Rd
@@ -20,19 +20,21 @@ comparing.
 The return list has three items:
 \describe{
-  \item{\code{FeatureData}}{Combined feature data from the provided SCESets.}
+    \item{\code{FeatureData}}{Combined feature data from the provided
-  \item{\code{PhenoData}}{Combined pheno data from the provided SCESets.}
+    SCESets.}
-  \item{\code{Plots}}{Comparison plots
+    \item{\code{PhenoData}}{Combined pheno data from the provided SCESets.}
-    \describe{
+    \item{\code{Plots}}{Comparison plots
-      \item{\code{Means}}{Violin plot of mean distribution.}
+        \describe{
-      \item{\code{Variances}}{Violin plot of variance distribution.}
+            \item{\code{Means}}{Violin plot of mean distribution.}
-      \item{\code{MeanVar}}{Scatter plot with fitted lines showing the
+            \item{\code{Variances}}{Violin plot of variance distribution.}
-      mean-variance relationship.}
+            \item{\code{MeanVar}}{Scatter plot with fitted lines showing the
-      \item{\code{LibraySizes}}{Boxplot of the library size distribution.}
+            mean-variance relationship.}
-      \item{\code{ZerosGene}}{Boxplot of the percentage of each gene that is
+            \item{\code{LibraySizes}}{Boxplot of the library size
-      zero.}
+            distribution.}
-      \item{\code{ZerosCell}}{Boxplot of the percentage of each cell that is
+            \item{\code{ZerosGene}}{Boxplot of the percentage of each gene
-      zero.}
+            that is zero.}
+            \item{\code{ZerosCell}}{Boxplot of the percentage of each cell
+            that is zero.}
    }
  }
 }

--- a/man/getParam.Rd
+++ b/man/getParam.Rd
@@ -21,4 +21,9 @@ The extracted parameter value
 \description{
 Accessor function for getting parameter values.
 }
+\examples{
+params <- newSimpleParams()
+getParam(params, "nGenes")
+}
--- a/man/logistic.Rd
+++ b/man/logistic.Rd
@@ -13,6 +13,9 @@ logistic(x, x0, k)
 \item{k}{shape parameter. Gives the slope of the function.}
 }
+\value{
+Value of logistic funciton with given parameters
+}
 \description{
 Implementation of the logistic function
 }

--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -35,4 +35,9 @@ Object with new parameter value.
 \description{
 Function for setting parameter values.
 }
+\examples{
+params <- newSimpleParams()
+setParam(params, "nGenes", 100)
+}