From cfbad4d54e82497a60ff9c4b940a804b2456eb38 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 29 Sep 2017 17:34:11 +1000
Subject: [PATCH] Update scDDEstimate
---
NAMESPACE | 1 +
R/scDD-estimate.R | 76 +++++++++++++++++++++++++--------------------
man/scDDEstimate.Rd | 26 ++++++++++------
3 files changed, 59 insertions(+), 44 deletions(-)
diff --git a/NAMESPACE b/NAMESPACE
index 216436b..16a874d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,6 +5,7 @@ S3method(lun2Estimate,matrix)
S3method(lunEstimate,SingleCellExperiment)
S3method(lunEstimate,matrix)
S3method(scDDEstimate,SingleCellExperiment)
+S3method(scDDEstimate,default)
S3method(scDDEstimate,matrix)
S3method(simpleEstimate,SingleCellExperiment)
S3method(simpleEstimate,matrix)
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index 7253c61..1ae1521 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -6,6 +6,8 @@
#' containing count data to estimate parameters from.
#' @param conditions Vector giving the condition that each cell belongs to.
#' Conditions can be 1 or 2.
+#' @param condition String giving the column that represents biological group of
+#' interest.
#' @param params SCDDParams object to store estimated values in.
#' @param verbose logical. Whether to show progress messages.
#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
@@ -29,64 +31,70 @@
#' }
#' @importFrom BiocParallel SerialParam
#' @export
-scDDEstimate <- function(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam()) {
+scDDEstimate <- function(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), ...) {
+
+ if (!requireNamespace("scDD", quietly = TRUE)) {
+ stop("The scDD simulation requires the 'scDD' package.")
+ }
+
UseMethod("scDDEstimate")
}
+#' @rdname scDDEstimate
+#' @importFrom SingleCellExperiment SingleCellExperiment
+#' @export
+scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), ...) {
+
+ checkmate::assertMatrix(counts, mode = "numeric", any.missing = FALSE,
+ min.rows = 1, min.cols = 1, row.names = "unique",
+ col.names = "unique")
+ checkmate::assertIntegerish(conditions, len = ncol(counts), lower = 1,
+ upper = 2)
+
+ counts <- SingleCellExperiment(assays = list(counts = counts),
+ colData = data.frame(condition = conditions))
+ scDDEstimate.default(counts, "condition", params, verbose, BPPARAM)
+}
+
#' @rdname scDDEstimate
#' @export
-scDDEstimate.SingleCellExperiment <- function(counts, conditions,
+scDDEstimate.SingleCellExperiment <- function(counts, condition = "condition",
params = newSCDDParams(),
verbose = TRUE,
- BPPARAM = SerialParam()) {
- counts <- BiocGenerics::counts(counts)
- scDDEstimate(counts, conditions, params, verbose, BPPARAM)
+ BPPARAM = SerialParam(), ...) {
+ scDDEstimate.default(counts, condition, params, verbose, BPPARAM)
}
#' @rdname scDDEstimate
#' @importFrom methods as
#' @export
-scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam()) {
-
- if (!requireNamespace("scDD", quietly = TRUE)) {
- stop("The scDD simulation requires the 'scDD' package.")
- }
+scDDEstimate.default <- function(counts, condition, params, verbose, BPPARAM) {
checkmate::assertClass(params, "SCDDParams")
- checkmate::assertMatrix(counts, mode = "numeric", any.missing = FALSE,
- min.rows = 1, min.cols = 1, row.names = "unique",
- col.names = "unique")
- checkmate::assertIntegerish(conditions, len = ncol(counts), lower = 1,
- upper = 2)
-
- counts.list <- list(Cond1 = counts[, conditions == 1],
- Cond2 = counts[, conditions == 2])
+ checkmate::assertClass(counts, "SingleCellExperiment")
+ checkmate::assertCharacter(condition, min.chars = 1, any.missing = FALSE,
+ len = 1)
+ if (!(condition %in% colnames(SummarizedExperiment::colData(counts)))) {
+ stop("'condition' must be the name of a column in `colData(counts)`")
+ }
if (verbose) {
- processed <- scDD::preprocess(counts.list, c("Cond1", "Cond2"),
- median_norm = TRUE)
+ processed <- scDD::preprocess(counts, condition, median_norm = TRUE)
} else {
suppressMessages(
- processed <- scDD::preprocess(counts.list, c("Cond1", "Cond2"),
- median_norm = TRUE)
+ processed <- scDD::preprocess(counts, condition, median_norm = TRUE)
)
}
- assays <- S4Vectors::SimpleList(NormCounts = processed)
-
- colData <- S4Vectors::DataFrame(condition = conditions,
- row.names = colnames(processed))
-
- SCdat <- SummarizedExperiment::SummarizedExperiment(assays = assays,
- colData = colData)
-
if (verbose) {
- SCdat <- scDD::scDD(SCdat, testZeroes = FALSE, param = BPPARAM)
+ SCdat <- scDD::scDD(processed, testZeroes = FALSE, param = BPPARAM,
+ condition = condition)
} else {
dummy <- utils::capture.output(suppressMessages(
- SCdat <- scDD::scDD(SCdat, testZeroes = FALSE, param = BPPARAM)
+ SCdat <- scDD::scDD(processed, testZeroes = FALSE, param = BPPARAM,
+ condition = condition)
))
}
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index 6eb052e..ca73df5 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -2,26 +2,26 @@
% Please edit documentation in R/scDD-estimate.R
\name{scDDEstimate}
\alias{scDDEstimate}
-\alias{scDDEstimate.SingleCellExperiment}
\alias{scDDEstimate.matrix}
+\alias{scDDEstimate.SingleCellExperiment}
+\alias{scDDEstimate.default}
\title{Estimate scDD simulation parameters}
\usage{
-scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE,
- BPPARAM = SerialParam())
-
-\method{scDDEstimate}{SingleCellExperiment}(counts, conditions,
- params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam())
+scDDEstimate(counts, params = newSCDDParams(), verbose = TRUE,
+ BPPARAM = SerialParam(), ...)
\method{scDDEstimate}{matrix}(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam())
+ verbose = TRUE, BPPARAM = SerialParam(), ...)
+
+\method{scDDEstimate}{SingleCellExperiment}(counts, condition = "condition",
+ params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(), ...)
+
+\method{scDDEstimate}{default}(counts, condition, params, verbose, BPPARAM)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
containing count data to estimate parameters from.}
-\item{conditions}{Vector giving the condition that each cell belongs to.
-Conditions can be 1 or 2.}
-
\item{params}{SCDDParams object to store estimated values in.}
\item{verbose}{logical. Whether to show progress messages.}
@@ -29,6 +29,12 @@ Conditions can be 1 or 2.}
\item{BPPARAM}{A \code{\link[BiocParallel]{BiocParallelParam}} instance
giving the parallel back-end to be used. Default is
\code{\link[BiocParallel]{SerialParam}} which uses a single core.}
+
+\item{conditions}{Vector giving the condition that each cell belongs to.
+Conditions can be 1 or 2.}
+
+\item{condition}{String giving the column that represents biological group of
+interest.}
}
\value{
SCDDParams object containing the estimated parameters.
--
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