Entering edit mode
Just a comment, not a complaint. The PDF file for the CummeRbund reference manual found at http://bioconductor.org/packages/2.11/bioc/html/cummeRbund.html has multiple occurrences of text running off the page.
I hope it's just my computer system, but in case it is not, I wanted to give newcomers a heads up.
Peter
For What It's Worth: Please use a more updated version of the package and manual. Bioconductor 2.11 is very old. Using release or devel instead of a hard coded Bioconductor version will ensure latest updates:
https://bioconductor.org/packages/release/bioc/html/cummeRbund.html