Many packages that do statistical analysis (such as DESeq2 or DEXSeq), use a design formula to specify the exact comparison. For example:

DESeqDataSet(se, design = ~ condition)

Where "condition" is the actual column name. I'd like to have the column name be adjustable. I tried using a variable in the formula:

design_col = "condition"
DESeqDataSet(se, design = ~ design_col)

As might be expected, that does not work ("all variables in design formula must be columns in colData"). I then tried:

design_col = "condition"
design_formula = paste("~", design_col)
DESeqDataSet(se, design = design_formula)

That also gives an error ("Error: $ operator is invalid for atomic vectors").

Is there a way to use variables in the design formula?

If you want to change the design programmatically you can do something like:

DESeqDataSet(se, design = formula(paste("~",x)))