[Bioc-devel] Alternative Hypothesis Specification For edgeR

[Aaron Lun]

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
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