I have sample information (sampleinfo) in this format:
SampleID condition type MP_1 A_1 Paired-End MP_2 A_1 Paired-End MP_3 A_1 Paired-End MN_1 A_2 Paired-End MN_2 A_2 Paired-End MN_3 A_2 Paired-End WP_1 B_1 Paired-End WP_2 B_1 Paired-End WP_3 B_1 Paired-End WN_1 B_2 Paired-End WN_2 B_2 Paired-End WN_3 B_2 Paired-End
I want to compare A_1 with A_2, B_1 with B_2 ans also want to compare (A_1+A_2) with (B_1+B_2).
This is how I used DESeqDataSetFromMatrix
ddsMat <- DESeqDataSetFromMatrix(countData = seqdata[,rownames(sampleinfo)], colData = sampleinfo, design = ~ condition) ddsMat <- DESeq(ddsMat) res.05_FC0<-results(ddsMat,contrast = c("condition","A_1","A_2"),alpha=0.05,lfcThreshold = 0) res.05_FC0<-results(ddsMat,contrast = c("condition","B_1","B_2"),alpha=0.05,lfcThreshold = 0)
How can I compare (A_1+A_2) with (B_1+B_2) using the contrast argument in results function?
Of course I can make a new sampleinfo table, but I want to use the same sampleinfo as above. I tried to read about numeric contrast, but I am unable to use it correctly.