as.data.frame() is also exported as an S3 method. Consequently, removing
as.data.table() method that has become redundant.keyType argument of GOaGO() is now optional. If not provided, keyType
attribute of genePairs, as set by annotateInteractions(), is used instead.New function annotateInteractions() to extract gene pairs from paired
genomic regions, along with helper functions annotateAnchors() and
convertTranscriptsToTSS().
Vignette section on the above, using example BEDPE file provided in
inst/extdata/.
Renamed parameter minTermPairs to minCount in GOaGO() and plotting
functions for consistency.
More readable default point shape and scale for point size in plotting functions.
Changed license from GPL (>= 3) to a more permissive Artistic-2.0.