From f5da0def91060a47cc15e114641706eda58e5902 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 13 Oct 2017 16:28:51 +1100
Subject: [PATCH] Run checks
---
DESCRIPTION | 3 ++-
R/BASiCS-estimate.R | 6 ++++--
man/BASiCSEstimate.Rd | 4 +++-
3 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 8d6ed5f..a57545e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -54,7 +54,8 @@ Suggests:
scran,
mfa,
phenopath,
- zinbwave
+ zinbwave,
+ BASiCS
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software
URL: https://github.com/Oshlack/splatter
diff --git a/R/BASiCS-estimate.R b/R/BASiCS-estimate.R
index 71932de..e29e6a0 100644
--- a/R/BASiCS-estimate.R
+++ b/R/BASiCS-estimate.R
@@ -30,13 +30,15 @@
#' @return BASiCSParams object containing the estimated parameters.
#'
#' @examples
+#' \dontrun{
#' data("sc_example_counts")
-#' spike.info <- data.frame(Name = rownames(counts)[1:10],
+#' spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
#' Input = rnorm(10, 500, 200),
#' stringsAsFactors = FALSE)
#' params <- BASiCSEstimate(sc_example_counts[1:50, 1:20],
#' spike.info)
#' params
+#' }
#' @export
BASiCSEstimate <- function(counts, spike.info = NULL, batch = NULL,
n = 20000, thin = 10, burn = 5000,
@@ -51,7 +53,7 @@ BASiCSEstimate.SCESet <- function(counts, spike.info = NULL, batch = NULL,
n = 20000, thin = 10, burn = 5000,
params = newBASiCSParams(), verbose = TRUE,
progress = TRUE, ...) {
- counts <- scater::counts(counts)
+ counts <- BiocGenerics::counts(counts)
BASiCSEstimate(counts, params)
}
diff --git a/man/BASiCSEstimate.Rd b/man/BASiCSEstimate.Rd
index 9309d89..0fabfeb 100644
--- a/man/BASiCSEstimate.Rd
+++ b/man/BASiCSEstimate.Rd
@@ -60,11 +60,13 @@ information is provided there must be at least two batches. See
\code{\link[BASiCS]{BASiCS_MCMC}} for details.
}
\examples{
+\dontrun{
data("sc_example_counts")
-spike.info <- data.frame(Name = rownames(counts)[1:10],
+spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
Input = rnorm(10, 500, 200),
stringsAsFactors = FALSE)
params <- BASiCSEstimate(sc_example_counts[1:50, 1:20],
spike.info)
params
}
+}
--
GitLab