CHANGES IN VERSION 1.3.9 ------------------------- NEW FEATURES * InteractionTrack class for plotting interactions with Gviz * plotAvgViewpoint for plotting summarised interactions around a set of features * summariseByFeaturePairs: to summarise interactions between all pairs of two feature sets SIGNIFICANT USER-LEVEL CHANGES * annotateInteractions is significantly faster * Data import has been made stricter and more consistent across different file formats. Homer interaction files now have data imported that was previously discarded. BUG FIXES * single viewpoint plotting (plotViewpoint) * is.dt, is.pt * calculateDistances * some import/export issues CHANGES IN VERSION 1.1.0 ------------------------- NEW FEATURES * Import method for reading data from two bam files containing paired end reads. * A function for removing duplicate interactions: 'removeDups' * Two methods for finding probable distance cutoffs for self ligations: 'get_binom_ligation_threshold' and 'get_self_ligation_threshold'. * 'countsBetweenAnchors': a function to summarise interactions between a set of genomic regions of interest. SIGNIFICANT USER-LEVEL CHANGES * GenomicInteractions objects have been refactored for consistency with GRanges objects. Interaction-level metadata such as p-values is now stored as a DataFrame accessible using 'mcols'. * importing data from a file is now done using 'makeGenomicInteractionsFromFile' * 'GenomicInteractions' can be used to construct a new object from anchors as GRanges objects and metadata. * 'show' method looks nicer and is faster. DEPRECATED AND DEFUNCT * 'FDR', 'pValue', 'normalisedCounts', 'genomeName': no longer needed because of refactoring. Access metadata by 'mcols' instead. * 'count' renamed to 'interactionCounts' BUG FIXES