Clarified docs.
Added mention of csaw, edgeR dependencies in comment boxes. Fiddled with require calls.
Got rid of an unncessary sort in savePairs.
Streamlined normalizeCNV interface, rotated marginal log-ratio space for better locfitting. Updated matching doc (with more elaboration), and version number.
Converted from log2 to log in returning offsets from normalizeCNV.
Finessed the continuity correction, to avoid errors when library sizes are different. Also set as prior count for aveLogCPM to retain linearity.
Merge branch 'master' into peakcalling