From 712fe45cc963c68626c382d799e2ba0e0ec26934 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Sun, 1 Oct 2017 15:20:56 +1100
Subject: [PATCH] Add mfaEstimate

---
 NAMESPACE          |  3 +++
 R/mfa-estimate.R   | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 man/mfaEstimate.Rd | 37 +++++++++++++++++++++++++++++++++++++
 3 files changed, 86 insertions(+)
 create mode 100644 R/mfa-estimate.R
 create mode 100644 man/mfaEstimate.Rd

diff --git a/NAMESPACE b/NAMESPACE
index dedc870..64df61f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,6 +4,8 @@ S3method(lun2Estimate,SingleCellExperiment)
 S3method(lun2Estimate,matrix)
 S3method(lunEstimate,SingleCellExperiment)
 S3method(lunEstimate,matrix)
+S3method(mfaEstimate,SingleCellExperiment)
+S3method(mfaEstimate,matrix)
 S3method(scDDEstimate,SingleCellExperiment)
 S3method(scDDEstimate,matrix)
 S3method(simpleEstimate,SingleCellExperiment)
@@ -23,6 +25,7 @@ export(lunSimulate)
 export(makeCompPanel)
 export(makeDiffPanel)
 export(makeOverallPanel)
+export(mfaEstimate)
 export(newLun2Params)
 export(newLunParams)
 export(newMFAParams)
diff --git a/R/mfa-estimate.R b/R/mfa-estimate.R
new file mode 100644
index 0000000..f3abf2f
--- /dev/null
+++ b/R/mfa-estimate.R
@@ -0,0 +1,46 @@
+#' Estimate mfa simulation parameters
+#'
+#' Estimate simulation parameters for the mfa simulation from a real dataset.
+#'
+#' @param counts either a counts matrix or a SingleCellExperiment object
+#'        containing count data to estimate parameters from.
+#' @param params MFAParams object to store estimated values in.
+#'
+#' @details
+#' The \code{nGenes} and \code{nCells} parameters are taken from the size of the
+#' input data. The dropout lambda parameter is estimate using
+#' \code{\link[mfa]{empirical_lambda}}. See \code{\link{MFAParams}} for more
+#' details on the parameters.
+#'
+#' @return MFAParams object containing the estimated parameters.
+#'
+#' @examples
+#' data("sc_example_counts")
+#' params <- mfaEstimate(sc_example_counts)
+#' params
+#' @export
+mfaEstimate <- function(counts, params = newMFAParams()) {
+    UseMethod("mfaEstimate")
+}
+
+#' @rdname mfaEstimate
+#' @export
+mfaEstimate.SingleCellExperiment <- function(counts,
+                                             params = newMFAParams()) {
+    counts <- BiocGenerics::counts(counts)
+    mfaEstimate(counts, params)
+}
+
+#' @rdname mfaEstimate
+#' @export
+mfaEstimate.matrix <- function(counts, params = newMFAParams()) {
+
+    checkmate::assertClass(params, "MFAParams")
+
+    dropout.lambda <- mfa::empirical_lambda(t(counts))
+
+    params <- setParams(params, nGenes = nrow(counts), nCells = ncol(counts),
+                        dropout.lambda = dropout.lambda)
+
+    return(params)
+}
diff --git a/man/mfaEstimate.Rd b/man/mfaEstimate.Rd
new file mode 100644
index 0000000..002cd04
--- /dev/null
+++ b/man/mfaEstimate.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mfa-estimate.R
+\name{mfaEstimate}
+\alias{mfaEstimate}
+\alias{mfaEstimate.SingleCellExperiment}
+\alias{mfaEstimate.matrix}
+\title{Estimate mfa simulation parameters}
+\usage{
+mfaEstimate(counts, params = newMFAParams())
+
+\method{mfaEstimate}{SingleCellExperiment}(counts, params = newMFAParams())
+
+\method{mfaEstimate}{matrix}(counts, params = newMFAParams())
+}
+\arguments{
+\item{counts}{either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.}
+
+\item{params}{MFAParams object to store estimated values in.}
+}
+\value{
+MFAParams object containing the estimated parameters.
+}
+\description{
+Estimate simulation parameters for the mfa simulation from a real dataset.
+}
+\details{
+The \code{nGenes} and \code{nCells} parameters are taken from the size of the
+input data. The dropout lambda parameter is estimate using
+\code{\link[mfa]{empirical_lambda}}. See \code{\link{MFAParams}} for more
+details on the parameters.
+}
+\examples{
+data("sc_example_counts")
+params <- mfaEstimate(sc_example_counts)
+params
+}
-- 
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