Add phenoEstimate

NAMESPACE

@@ -6,6 +6,8 @@ S3method(lunEstimate,SingleCellExperiment)
 S3method(lunEstimate,matrix)
 S3method(mfaEstimate,SingleCellExperiment)
 S3method(mfaEstimate,matrix)
+S3method(phenoEstimate,SingleCellExperiment)
+S3method(phenoEstimate,matrix)
 S3method(scDDEstimate,SingleCellExperiment)
 S3method(scDDEstimate,default)
 S3method(scDDEstimate,matrix)
@@ -35,6 +37,7 @@ export(newPhenoParams)
 export(newSCDDParams)
 export(newSimpleParams)
 export(newSplatParams)
+export(phenoEstimate)
 export(phenoSimulate)
 export(scDDEstimate)
 export(scDDSimulate)

R/pheno-estimate.R

+#' Estimate PhenoPath simulation parameters
+#'
+#' Estimate simulation parameters for the PhenoPath simulation from a real
+#' dataset.
+#'
+#' @param counts either a counts matrix or an SingleCellExperiment object
+#'        containing count data to estimate parameters from.
+#' @param params PhenoParams object to store estimated values in.
+#'
+#' @details
+#' The \code{nGenes} and \code{nCells} parameters are taken from the size of the
+#' input data. The total number of genes is evenly divided into the four types.
+#' See \code{\link{PhenoParams}} for more details on the parameters.
+#'
+#' @return PhenoParams object containing the estimated parameters.
+#'
+#' @examples
+#' data("sc_example_counts")
+#' params <- phenoEstimate(sc_example_counts)
+#' params
+#' @export
+phenoEstimate <- function(counts, params = newPhenoParams()) {
+    UseMethod("phenoEstimate")
+}
+
+#' @rdname phenoEstimate
+#' @export
+phenoEstimate.SingleCellExperiment <- function(counts,
+                                               params = newPhenoParams()) {
+    counts <- BiocGenerics::counts(counts)
+    phenoEstimate(counts, params)
+}
+
+#' @rdname phenoEstimate
+#' @export
+phenoEstimate.matrix <- function(counts, params = newPhenoParams()) {
+
+    checkmate::assertClass(params, "PhenoParams")
+
+    nGenes <- nrow(counts)
+    quarter <- floor(nGenes / 4)
+
+    params <- setParams(params, nCells = ncol(counts),
+                        n.de = nGenes - 3 * quarter,
+                        n.pst = quarter, n.pst.beta = quarter,
+                        n.de.pst.beta = quarter)
+
+    return(params)
+}

man/phenoEstimate.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pheno-estimate.R
+\name{phenoEstimate}
+\alias{phenoEstimate}
+\alias{phenoEstimate.SingleCellExperiment}
+\alias{phenoEstimate.matrix}
+\title{Estimate PhenoPath simulation parameters}
+\usage{
+phenoEstimate(counts, params = newPhenoParams())
+
+\method{phenoEstimate}{SingleCellExperiment}(counts,
+  params = newPhenoParams())
+
+\method{phenoEstimate}{matrix}(counts, params = newPhenoParams())
+}
+\arguments{
+\item{counts}{either a counts matrix or an SingleCellExperiment object
+containing count data to estimate parameters from.}
+
+\item{params}{PhenoParams object to store estimated values in.}
+}
+\value{
+PhenoParams object containing the estimated parameters.
+}
+\description{
+Estimate simulation parameters for the PhenoPath simulation from a real
+dataset.
+}
+\details{
+The \code{nGenes} and \code{nCells} parameters are taken from the size of the
+input data. The total number of genes is evenly divided into the four types.
+See \code{\link{PhenoParams}} for more details on the parameters.
+}
+\examples{
+data("sc_example_counts")
+params <- phenoEstimate(sc_example_counts)
+params
+}