diff --git a/DESCRIPTION b/DESCRIPTION index dd43712..1380561 100644 --- 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 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 index 6c25dee..9b5e182 100644 --- 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) ```