Suppose I have run deseq like this:

my_coldata$varA = factor(mycoldata$varA, levels=c('control', 'case')
my_coldata$varB = factor(mycoldata$varB, levels=c(0,1))

dds =  DESeqDataSetFromMatrix(
    countData=my_counts,
    colData=my_coldata,
    design=~varA + varB
  )

deseq_obj = DESeq(
    dds,
    test='Wald',
    fitType='mean'
  )

I can access the metadata with colData(deseq_obj) but it comes as a matrix with factor and level information wiped out. Is there a way to access this information?

Maybe a suggestion would be to switch to DataFrames since that is becoming ever more standard in the r-verse.

Thanks!

Check out the SummarizedExperiment package for details on how colData works. It is in fact a DataFrame.

You can just do dds$variable to print the variable and if it is a factor it will print the levels.