Bug fix to seqinfo<- to support other arguments in the generic.
Modified behaviour of inflate() with unspecified fill= for GInteractions objects.
Updated show() methods for GInteractions objects.
Supported Hits inputs for repeated linkOverlaps() calls. Set ignore.strand=TRUE by default.
findOverlaps() with no subject argument now returns a SortedBySelfQueryHits.
Removed c() method for InteractionSet, rbind method for GInteractions.
Generalized ContactMatrix to allow any type of matrix-like object.
Supported inflate() for GInteractions without specifying fill. Changed default fill for InteractionSet to missing.
Separated subsetting and combining documentation into two different pages.
Added convenience wrappers for resize(), narrow() and shift() on the GenomicRanges slot in all objects.
Modified anchors() to return a list rather than GRangesList.
Modified width() for GInteractions to return a list() rather than a DataFrame(). Also changed names of list element.
Added the anchorIds() function for rapid extraction of anchor IDs.
Removed the requirement for identical regions in pcompare() and match().
Deprecated anchors<- in favour of anchorIds<-, to avoid confusion about 'value' type.
Added first(), second() functions for convenience.
Updates to documentation, tests.
Allowed specification of NULL in row/column arguments to inflate().
Fixes to tests and code in response to updates to BiocGenerics, S4Vectors.
Added CITATION to the F1000Res article.
New package InteractionSet, containing base classes for genomic interaction data.