Move example code form the usage section to the examples section.
updated version and date
documented non-core elements of the result variable.
Removed references to the GitHub tutorial, out of date, and better replaced by the UsersGuide.
Removed duplicate filtering for Biological process. Added a comment to make the point that shortcuts exist for filtering.
Replaced equals by arrows in vignette, plus cleaning parameter values.
Replaced all occurences of log2cpm and targets by AlvMac, in examples, documentation, and code.