For downstream analysis using a modified version of Robust Rank Aggregation (alpha-RRA; Li, et al. Genome Biology 2014), I would like to obtain one-tailed p-values from a standard DESeq2 analysis using a Wald test (rather than the two-tailed p-values that are represented in a 'DESeqResults' object). Can this be done from a 'DESeqDataSet' or a 'DESeqResults' object using DESeq2, and if so what steps should I take to do that?

Thanks, Thomas

See the vignette section on threshold tests. You would set lfcThreshold to 0 and specify the alternative as less than or greater than.