Make collapseFullCoverage a tiny bit more efficient by not using names
v0.0.60 Working on regionMatrix() -- updated README
Added two new arguments to regionMatrix() to normalize the data prior to filtering. Added more verbose output
Made more robust for cases where there is no chrX. Also now uses UCSC seqnames
Uses UCSC seqlevelsStyle now
Dropped 'addChrPrefix' and added 'levelsStyle' to makeGenomicState()
Now uses mapSeqlevels() to use UCSC names for automatic output
fullCoverage() 'chrnums' changed to 'chrs' as mapSeqlevels() is now used
Use integers for p and nVec
Minor tweaks, including dropping gc() calls
Introduced the 'chrsStyle' argument in several functions. This makes derfinder more robust to different chr naming conventions
Removed some gc() calls
Added the chrsStyle argument which is passed to findRegions()
Now has the chrsStyle argument
analyzeChr() and mergeResults() now have the 'chrsStyle' argument. Minor tweaks to a few other functions. Added a warning for analyzeChr() when cutoffType = 'empirical' but cutoffFstat is not updated.
Removed a couple of gc calls
Updated NEWS
Added a comment
No need to use verbose in this case since it only prints a dot for every chr analyzed and the function is already running at a chr level
Removed the last gc() calls left. Thus complying with the recommendation from http://adv-r.had.co.nz/memory.html that no gc() calls should be made as it's not really beneficial. Left rm() calls whenever there are still other calculations steps to go before the end of the function. That is, removed rm() calls just before a return() call.