How to add a second covariate in the analysis? age is the covariate in my design. I would also like to add sex to it. I looked at some of the answers but I am not sure they exactly explain what I am looking for? Would just adding it after age solve this?

Code should be placed in three backticks as shown below

dds <- DESeqDataSetFromTximport(txi, sampleTable, ~age +condition)

The formula for DESeq2 works in the same way as any formula that we specify in R. The y variable is essentially the gene's expression, with predictors / covariates as x variables:

gene ~ age + condition

Thus, if you want to adjust for more covariates, just use something like:

~ age + sex + smoking + condition

Then, when deriving test statistics, check the coefficient names via resultsNames(dds) in order to ensure that you extrapolate the correct stats.

Kevin