Hello,
When doing a gene ontology analysis, it is common to remove gene sets that are
small to avoid a problem of their statistics spuriously being significant. For
example, I have a list of 681 significantly differentially expressed genes, but
some expected overlap values are much smaller than 1.
> head(GOsummary)
GO ID Term Overlap Expected Overlap
1 GO:0051591 response to cAMP 4 0.06257822
2 GO:0046683 response to organophosphorus 4 0.08635795
3 GO:0014074 response to purine-containing compound 4 0.10137672
4 GO:1901700 response to oxygen-containing compound 7 0.99374218
5 GO:0035914 skeletal muscle cell differentiation 3 0.05256571
6 GO:0009725 response to hormone 6 0.64205257
This functionality is missing. Also, in the documentation of the constructor of
GOHyperGParams, there is no description of what ... is for. Although it can
accept variables with the same names as the slots, this is not explained. It
would be good if there was a real constructor, instead of the user calling new
explicitly.
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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