From 41b26675abdbbd8391148d9ab30148d49921ab1e Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 20 Aug 2019 16:50:55 +1000
Subject: [PATCH] Fix parameter passing in BASiCSEstimate
Parameters were not being passed from the SingleCellExperiment method to the
matrix method
---
R/BASiCS-estimate.R | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/R/BASiCS-estimate.R b/R/BASiCS-estimate.R
index f3148ed..229cddf 100644
--- a/R/BASiCS-estimate.R
+++ b/R/BASiCS-estimate.R
@@ -35,13 +35,13 @@
#' \dontrun{
#' # Load example data
#' library(scater)
-#' data("sc_example_counts")
+#' set.seed(1)
+#' sce <- mockSCE()
#'
-#' spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
+#' spike.info <- data.frame(Name = rownames(sce)[1:10],
#' Input = rnorm(10, 500, 200),
#' stringsAsFactors = FALSE)
-#' params <- BASiCSEstimate(sc_example_counts[1:100, 1:30],
-#' spike.info)
+#' params <- BASiCSEstimate(sce[1:100, 1:30], spike.info)
#' params
#' }
#' @export
@@ -63,7 +63,8 @@ BASiCSEstimate.SingleCellExperiment <- function(counts, spike.info = NULL,
verbose = TRUE, progress = TRUE,
...) {
counts <- BiocGenerics::counts(counts)
- BASiCSEstimate(counts, params)
+ BASiCSEstimate(counts, spike.info, batch, n, thin, burn, regression,
+ params, verbose, progress, ...)
}
#' @rdname BASiCSEstimate
--
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