P-value cutoff _also_ applied to adjusted P-value

[kevinrue]

https://github.com/GuangchuangYu/DOSE/blob/01913f001ad7ea0808a61e30f7f5943a84c3a23f/R/gsea.R#L57

As a user, I would not expect pvalueCutoff to be applied to the p.adjust column. Or at least I think it should be made clear in the documentation that pvalueCutoff is not only applied to the pvalue column, but also the p.adjust column. In addition, given that we have always p.adjust >= pvalue, it might as well be documented as "adjusted pvalue cutoff".

That said, as an experienced R user and considering from the code that the only purpose of this cutoff value is to subset the result table, I would simply set pvalueCutoff=1 to get the full table and do the filtering myself.

I'm only reporting this unexpected behaviour for unsuspecting and less experienced users.