Ah - sorry - upon re-reading your message, I realized I misunderstood your question. So basically you want to make your LRT p-value one-sided; I can see how that would be useful, e.g., when comparing to negative controls in ChIP-seq or other technologies.
I've been doing it fairly simply, exploiting the asymptotic independence of the test result from the sign of the log-fold change: is.up <- result$table$logFC > 0 os.p <- result$table$PValue/2 os.p[!is.up] <- 1 - os.p[!is.up] ... which seemed short enough to do manually. I suppose we could add this as an option to glmLRT, if it seems useful. Cheers, Aaron On 16/01/17 04:00, Dario Strbenac wrote: > Good day, > > In a future release, could the user be allowed to specify an alternative > hypothesis such as the coefficient being positive? DESeq2 provides an > altHypothesis parameter for such a purpose. > > -------------------------------------- > Dario Strbenac > University of Sydney > Camperdown NSW 2050 > Australia > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
