[BioC] (minfi) Return value from dmpFinder

[Gustavo Fernández Bayón]

Hi everybody. 

I am currently using minfi for every analysis of Illumina 450k I am working on. But today I have run into what I consider a minor problem, i.e., more a matter of usability IMHO.

Problem is, dmpFinder returns a data.frame with columns for the statistic, the p-value, the q-value and the intercept. And, if I would like to know which CpG's are hyper- or hypo-methylated from that table, I think I couldn't (I am talking about the two-category case here). For that, I would need the value of the second coefficient of the model, the actual slope of the fit. 

Besides, I would need to know the order of the levels in the factor used as a phenotype indicator (remember two categories case here), in order to interpret the sign of the slope. And minfi is executing:

pheno <- factor(as.character(pheno))

which makes the previous ordering of the levels go away. I understand the general behavior of dmpFinder, and why its result is the way it is, but shouldn't it be a good idea to act differently in this case? I think that comparison of two groups, and splitting between hyper and hypo-methylated probes is very common. 

For now, I think I'll do the t-test, correct with p.adjust, and get the values I need on the fly.

Regards,
Gustavo


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