How to change the design DESeqDataSet to calculate log2foldChange in different way?

Question

[Amr]

How to change the design DESeqDataSet to calculate log2foldChange in different way? for example the log fold change condition: Normal vs Mutated, How to make it Mutated vs Normal?

countdata2<- subset(countdata, select=c("WM793_rep1","WM793_rep2","NHEM_rep1", "NHEM_rep2"))

coldata2<data.frame("condition"=as.factor(c(rep("Mutated",2),rep("Normal",2))),row.names=colnames(countdata2))

dds2 <- DESeqDataSetFromMatrix(countData = countdata2, colData =coldata2,design = ~condition )

dds2 <- DESeq(dds2)

Thanks in advance

Answer 1

[Amr]

The answer is to add contrast parameter and add the desired ordering :

results(dds3,contrast = c("condition","Mutated","Normal"))