Fix bugs in vignette

scater normalise renamed to normalize

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.7.0
-Date: 2018-10-22
+Version: 1.7.1
+Date: 2018-11-17
 Author: Luke Zappia
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),
@@ -66,6 +66,6 @@ biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
     Software
 URL: https://github.com/Oshlack/splatter
 BugReports: https://github.com/Oshlack/splatter/issues
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 Encoding: UTF-8
 VignetteBuilder: knitr

NEWS.md

+## Version 1.7.1 (2018-11-17)
+
+* Fix bugs in vignette
+
 ## Version 1.7.0 (2018-11-01)
 
 Bioconductor 3.9 devel

vignettes/splatter.Rmd

@@ -283,7 +283,7 @@ in `scater`. For example we can make a PCA plot:
 
 ```{r pca}
 # Use scater to calculate logcounts
-sim <- normalise(sim)
+sim <- normalize(sim)
 # Plot PCA
 plotPCA(sim)
 ```
@@ -343,7 +343,7 @@ printing progress messages.)
 ```{r groups}
 sim.groups <- splatSimulate(group.prob = c(0.5, 0.5), method = "groups",
                             verbose = FALSE)
-sim.groups <- normalise(sim.groups)
+sim.groups <- normalize(sim.groups)
 plotPCA(sim.groups, colour_by = "Group")
 ```
 
@@ -362,7 +362,7 @@ method.
 
 ```{r paths}
 sim.paths <- splatSimulate(method = "paths", verbose = FALSE)
-sim.paths <- normalise(sim.paths)
+sim.paths <- normalize(sim.paths)
 plotPCA(sim.paths, colour_by = "Step")
 ```
 
@@ -382,7 +382,7 @@ cells are in each batch:
 
 ```{r batches}
 sim.batches <- splatSimulate(batchCells = c(50, 50), verbose = FALSE)
-sim.batches <- normalise(sim.batches)
+sim.batches <- normalize(sim.batches)
 plotPCA(sim.batches, colour_by = "Batch")
 ```
 
@@ -396,7 +396,7 @@ that we aren't interested in (batch) and the wanted variation we are looking for
 ```{r batch-groups}
 sim.groups <- splatSimulate(batchCells = c(50, 50), group.prob = c(0.5, 0.5),
                             method = "groups", verbose = FALSE)
-sim.groups <- normalise(sim.groups)
+sim.groups <- normalize(sim.groups)
 plotPCA(sim.groups, shape_by = "Batch", colour_by = "Group")
 ```