Set up basic structure of splat function

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.3.1
-Date: 2016-10-07
+Version: 0.3.2
+Date: 2016-10-09
 Author: Luke Zappia
 Authors@R: as.person(c(
     "Luke Zappia <luke.zappia@mcri.edu.au> [aut, cre]",

NAMESPACE

@@ -10,6 +10,10 @@ export(getParams)
 export(mergeParams)
 export(setParams)
 export(splatParams)
+importFrom(BioBase,fData)
+importFrom(BioBase,pData)
+importFrom(scater,counts)
+importFrom(scater,newSCESet)
 importFrom(stats,dnbinom)
 importFrom(stats,median)
 importFrom(stats,nls)

R/simulate.R

+# setup metadata
+# Means
+# Groups
+# Paths
+# Lib size
+# Base Means
+# BCV
+# Means
+# Counts
+# Dropout
+# Add metadata
+#
+# Add length
+# Median outliers
+# set.seed
+# group DE
+
+
+
+#' FUNCTION TITLE
+#'
+#' FUNCTION DESCRIPTION
+#'
+#' @param params DESCRIPTION.
+#' @param method DESCRIPTION.
+#' @param add.assay DESCRIPTION.
+#' @param verbose DESCRIPTION.
+#' @param ... DESCRIPTION.
+#'
+#' @return RETURN DESCRIPTION
+#' @examples
+#' # ADD EXAMPLES HERE
+#' @importFrom BioBase pData fData
+#' @importFrom scater newSCESet counts
+splat <- function(params = defaultParams(), method = c("groups", "paths"),
+                  add.assay = TRUE, verbose = TRUE, ...) {
+
+    method <- match.arg(method)
+
+    params <- setParams(params, ...)
+    params <- mergeParams(params, defaultParams())
+
+    # Get the parameters we are going to use
+    n.cells <- getParams(params, "nCells")
+    n.genes <- getParams(params, "nGenes")
+    n.groups <- getParams(params, "nGroups")
+    group.cells <- getParams(params, "groupCells")
+
+    # Set up name vectors
+    cell.names <- paste0("Cell", 1:n.cells)
+    gene.names <- paste0("Gene", 1:n.genes)
+    group.names <- paste0("Group", 1:n.groups)
+
+    # Create SCESet with dummy counts to store simulation
+    dummy.counts <- matrix(1, ncol = n.cells, nrow = n.genes)
+    rownames(dummy.counts) <- gene.names
+    colnames(dummy.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))
+    rownames(features) <- gene.names
+    sim <- newSCESet(countData = dummy.counts, phenoData = phenos,
+                     featureData = features)
+
+    # Make groups vector which is the index of param$groupCells repeated
+    # params$groupCells[index] times
+    groups <- lapply(1:n.groups, function(i, g) {rep(i, g[i])},
+                     g = group.cells)
+    groups <- unlist(groups)
+    pData(sim)$Group <- group.names[groups]
+
+    # Create new SCESet to make sure values are calculated correctly
+    sce <- newSCESet(countData = counts(sim),
+                     phenoData = new("AnnotatedDataFrame", data = pData(sim)),
+                     featureData = new("AnnotatedDataFrame", data = fData(sim)))
+
+    return(sce)
+}
\ No newline at end of file

man/splat.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/simulate.R
+\name{splat}
+\alias{splat}
+\title{FUNCTION TITLE}
+\usage{
+splat(params = defaultParams(), method = c("groups", "paths"),
+  add.assay = TRUE, verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{DESCRIPTION.}
+
+\item{method}{DESCRIPTION.}
+
+\item{add.assay}{DESCRIPTION.}
+
+\item{verbose}{DESCRIPTION.}
+
+\item{...}{DESCRIPTION.}
+}
+\value{
+RETURN DESCRIPTION
+}
+\description{
+FUNCTION DESCRIPTION
+}
+\examples{
+# ADD EXAMPLES HERE
+}
+

man/splatParams.Rd

@@ -23,6 +23,7 @@ parameters. It has the following sections and values:
 \itemize{
   \item nGenes - Number of genes to simulate.
   \item nCells - Number of cells to simulate.
+  \item nGroups - Number of groups to simulate.
   \item [groupCells] - Vector giving the number of cells in each simulation
         group/path.
   \item mean (mean parameters)