Finished calculateStats() and helper functions fstats.apply(), fstats(). makeCoverage() is very similar to makeDF() from derfinder 1.0.2 with the difference that it now uses filterData(); filterData() is also  used by calculateStats(). Will soon remove the BSgenome code from makeCoverage(). This version has example data and all the functions have examples although a vignette is missing.
Separated fstats.apply() into it's own file
Tweaked fstats.apply() to correctly test in the case that comparison='expression'
Modifying the data matrix in Rle world instead of each chunk. Note that calculateStats(comparison='expression') is not really implemented yet.
Renamed makeCoverage()
Finished modified makeCoverage() to loadCoverage() using Andrew Jaffe's input for dropping the dependencies on BSgenome
Greatly improved the NAMESPACE via roxygen2 documentation. Changed the dependencies using the Bioconductor guidelines. Fixed the require() calls by changing them to library(). Specified a license (Artistic-2.0) by following what bumphunter specifies. The namespace changes improved the speed of the loadCoverage() example: 5s to 3s. R CMD check passes cleanly! Added biocViews following DEXSeq and bumphunter's guide.
Implemented regionFinder() from bumhunter using Rle's. The speed is a tad slower, but in theory it allows the user to reduce the memory of the objects (s)he has to save. The runtime memory would be less if which(statsInfo) could be avoided in findRegions(). Namespace is completely specified, all man pages are complete. Missing: a vignette.
Minor fix to loadCoverage()
Updated the automatic name
Implemented calculatePvalues() that runs most of the other functions. Some arguments changed to make things more efficient in calculatePvalues().
Changed how the data was being processed in calculateStats() to pass only the actual subset of interest to fstats.apply(). This reduces memory usage, specially when considering that chr1 is nearly 1GB in memory. Added literature references and double checked man pages via quick visual inspection.
Minor warning fix
Added plots for calculatePvalues() output and it will now return the nullstats as well for further downstream use.
Explained better that calculatePvalues() is
Modified verbose messages by adding date() to them. Will be useful when running the larger chrs and getting and idea of which parts are slower.
Minor tweak to the pvalues calculation