I want to compare the DEG expression levels in WT(Wild Type) and three mutants(mutantA, mutantB, mutantC ; lacked a certain genes). I used Salmon, tximport, and DESeq2(shown below).

group <- data.frame(con = (c(rep("WT", 3), rep("A", 3), rep("B", 3), rep("C", 3)))

# compare WT with A
dds <- DESeqDataSetFromTximport(txi = gene.exp, colData = group, design = ~ con)
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
dds <- nbinomWaldTest(dds)
res <- results(dds, contrast = c("con", "WT", "A"))
head(res[order(res$pvalue), ])
write.table(res, file = "result.txt", row.names = T, col.names = T, sep = "\t")

# compare WT with B
dds <- DESeqDataSetFromTximport(txi = gene.exp, colData = group, design = ~ con)
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
dds <- nbinomWaldTest(dds)
res <- results(dds, contrast = c("con", "WT", "B"))
head(res[order(res$pvalue), ])
write.table(res, file = "result.txt", row.names = T, col.names = T, sep = "\t")

# compare WT with C
dds <- DESeqDataSetFromTximport(txi = gene.exp, colData = group, design = ~ con)
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
dds <- nbinomWaldTest(dds)
res <- results(dds, contrast = c("con", "WT", "C"))
head(res[order(res$pvalue), ])
write.table(res, file = "result.txt", row.names = T, col.names = T, sep = "\t")

dds <- DESeqDataSetFromTximport(txi = gene.exp, colData = group, design = ~ con)
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
dds <- nbinomLRT(dds, full = ~ con, reduced = ~ 1)
res <- results(dds)
head(res[order(res$pvalue), ])
write.table(res, file = "result.txt", row.names = T, col.names = T, sep = "\t")

Is this correct? Should I do something for WT?

Would you tell me the workflow?