nbinomLRT shouldn't be called directly

statOmics · Aug 7, 2018 · a2bfbac · a2bfbac
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: stageR
 Type: Package
 Title: stageR: stage-wise analysis of high throughput gene expression data in R
-Version: 1.3.26
+Version: 1.3.27
 Author: Koen Van den Berge and Lieven Clement
 Maintainer: Koen Van den Berge <[email protected]>
 Description: The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published in Genome Biology at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0

diff --git a/vignettes/stageRVignette.Rmd b/vignettes/stageRVignette.Rmd
@@ -205,7 +205,7 @@ dxd <- DEXSeqDataSet(countData = exprs(esetProstate),
                      groupID = as.character(geneForEachTx))
 dxd <- estimateSizeFactors(dxd)
 dxd <- estimateDispersions(dxd)
-dxd <- nbinomLRT(dxd, reduced=~ sample + exon + patient)
+dxd <- testForDEU(dxd, reducedModel=~ sample + exon + patient)
 dxr <- DEXSeqResults(dxd)
 qvalDxr <- perGeneQValue(dxr)
 ```