Changes

The G test of independence is now used both at the gene level and the transcript level. This means that the gene-level tests perform a single test of independence per gene, instead of two tests of goodness of fit, and the transcript-level tests are no longer based on R's prop.test() and chiqs.test(). Additionally, this clarifies and simplifies the testing procedure. No continuity corrections are applied in either case.
As a consequence of 1., the Genes table now has a single set of fields, instead of duplicate fields suffixed by AB and BA. This should not affect usage, unless you were explicitly accessing these fields.
As a consequence of 1., the FPR should be slightly reduced for both gene-level calls and transcript-level calls.
As a consequence of 1., the number of tests executed for the gene-level calls is halved and should result in a noticeable boost in speed.
rboot is now by default FALSE.
The previously exported g.test() (goodness of fit) is now replaced by g.test.1() (goodness of fit) and g.test.2() (independence). This prevents potential naming clash with more general-purpose g.test functions provided by other third-party packages. Both are heavily stripped down for efficiency and leave all data validity checks to the user. RATs only uses the version for test of independence. The goodness of fit version may get deprecated in future releases.

New features

Added: functions to get tally and IDs of genes/transcripts implicated in isoform-switching. This report will also be displayed at the end of a verbose run.