From 5e63dfce9f7d924eb021883bb20cb56e7dbf568d Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Sun, 1 Oct 2017 17:33:44 +1100
Subject: [PATCH] Run checks
---
R/scDD-estimate.R | 20 +++++++++++++-------
man/scDDEstimate.Rd | 13 ++++++++-----
2 files changed, 21 insertions(+), 12 deletions(-)
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index 1ae1521..9c21367 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -13,6 +13,7 @@
#' @param 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.
+#' @param ... further arguments passed to or from other methods.
#'
#' @details
#' This function applies \code{\link[scDD]{preprocess}} to the counts then uses
@@ -31,8 +32,9 @@
#' }
#' @importFrom BiocParallel SerialParam
#' @export
-scDDEstimate <- function(counts, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam(), ...) {
+scDDEstimate <- function(counts, #conditions, condition,
+ params = newSCDDParams(), verbose = TRUE,
+ BPPARAM = SerialParam(), ...) {
if (!requireNamespace("scDD", quietly = TRUE)) {
stop("The scDD simulation requires the 'scDD' package.")
@@ -44,8 +46,9 @@ scDDEstimate <- function(counts, params = newSCDDParams(),
#' @rdname scDDEstimate
#' @importFrom SingleCellExperiment SingleCellExperiment
#' @export
-scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam(), ...) {
+scDDEstimate.matrix <- function(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(),
+ conditions, ...) {
checkmate::assertMatrix(counts, mode = "numeric", any.missing = FALSE,
min.rows = 1, min.cols = 1, row.names = "unique",
@@ -60,17 +63,20 @@ scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
#' @rdname scDDEstimate
#' @export
-scDDEstimate.SingleCellExperiment <- function(counts, condition = "condition",
+scDDEstimate.SingleCellExperiment <- function(counts,
params = newSCDDParams(),
verbose = TRUE,
- BPPARAM = SerialParam(), ...) {
+ BPPARAM = SerialParam(),
+ condition = "condition", ...) {
scDDEstimate.default(counts, condition, params, verbose, BPPARAM)
}
#' @rdname scDDEstimate
#' @importFrom methods as
#' @export
-scDDEstimate.default <- function(counts, condition, params, verbose, BPPARAM) {
+scDDEstimate.default <- function(counts,
+ params = newSCDDParams(), verbose = TRUE,
+ BPPARAM = SerialParam(), condition, ...) {
checkmate::assertClass(params, "SCDDParams")
checkmate::assertClass(counts, "SingleCellExperiment")
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index ca73df5..2651834 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -10,13 +10,14 @@
scDDEstimate(counts, params = newSCDDParams(), verbose = TRUE,
BPPARAM = SerialParam(), ...)
-\method{scDDEstimate}{matrix}(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam(), ...)
+\method{scDDEstimate}{matrix}(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), conditions, ...)
-\method{scDDEstimate}{SingleCellExperiment}(counts, condition = "condition",
- params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(), ...)
+\method{scDDEstimate}{SingleCellExperiment}(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), condition = "condition", ...)
-\method{scDDEstimate}{default}(counts, condition, params, verbose, BPPARAM)
+\method{scDDEstimate}{default}(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), condition, ...)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
@@ -30,6 +31,8 @@ containing count data to estimate parameters from.}
giving the parallel back-end to be used. Default is
\code{\link[BiocParallel]{SerialParam}} which uses a single core.}
+\item{...}{further arguments passed to or from other methods.}
+
\item{conditions}{Vector giving the condition that each cell belongs to.
Conditions can be 1 or 2.}
--
GitLab