NEWS

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GenomicInteractions 1.5.3

NEW FEATURES

• Integration with the new InteractionSet package provides new features including more overlaps methods and conversion to other classes for storing genomic interaction data. See InteractionSet documentation for more details.

SIGNIFICANT USER-LEVEL CHANGES

• Following InteractionSet integration, distance calculation is done differently and some distances may differ by 1bp.

DEPRECATED AND DEFUNCT

• 'annotateAnchors' is deprecated and replaced by 'annotateRegions'.

GenomicInteractions 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