Added the readMTX2IntSet() function to create InteractionSets from file.
Extended prunePairs() to acknowledge restrict, discard and cap in param= argument.
Extended getPairs() to acknowledge restrict, discard and cap in param= argument.
Added restrict.regions= option to connectCounts(), squareCounts().
Removed unnecessary normalize() export.
Upgraded presplit_map.py, iter_map.py to run on Python 3 and to use Bio.SeqIO.parse().
Added extractPatch() function to count bin pairs in a specified area of the interaction space.
Modified connectCounts() to eliminate warnings upon stranded entries, unknown chromosomes. All entries of input regions are now retained, though not necessarily in the input order. Also switched original metadata to NA when second.regions is an integer.
Modified preparePairs() to be more generous when considering inward-facing reads if they overlap past each other.
Fixed bug in savePairs() involving failure to swap other information when enforcing index ordering.
Added mergeCMs() function to allow entry into the pipeline from ContactMatrix objects.
Moved pre-processing scripts out of the package to the repository for the user's guide.
Updated presplit_map.py to use new samtools API for sorting.
Updated user's guide.
Streamlined filterDirect(), filterTrended(), and added tests for them. Also allowed specification of which assay to use for the data and reference objects.
enrichedPairs() and neighborCounts() now return counts for neighbourhood regions, not just the enrichment values.
filterPeaks() will compute (and optionally return) enrichment values from neighbourhood counts.
normalizeCNV() and correctedContact() allow specification of which assay matrix to use from the SE objects.
Refactored a great deal of the C++ code for improved clarity.
Overhauled handling of DNase Hi-C data, so that pseudo-fragments are no longer necessary. Most functions now automatically recognise DNase-C data from an empty GRanges in param$fragments. Deprecated segmentGenome() and prepPseudoPairs(), added the emptyGenome() function.
Updated user's guide.
Relaxed checks in preparePairs(), prepPseudoPairs() when more chromosomes are supplied than needed.
Relaxed checks in connectCounts() when extra chromosomes are in the input ranges.
Fixed an issue with preparePairs() when too many file handles are open.
Fixed clash between BiocGenerics and Matrix which().
Modified domainDirections() to return a RangedSummarizedExperiment.
Removed defunct DIList class and methods.
Switched from seqlevels() to seqlevelsInUse() for fragment intervals.
Updated user's guide, documentation.
Deprecated DIList objects and methods in favour of InteractionSet objects.
marginCounts() now returns a RangedSummarizedExperiment for all bins.
Added the max.height argument to the rotPlaid() and rotDI() functions.
Added the diClusters() function for post-hoc cluster-level FDR control.
Added the annotatePairs() function for convenient annotation of (clusters of) interactions.
Fixed a bug in plotPlaid() when the interaction space was empty.
Fixed a bug in preparePairs() where unmapped chimeric segments led to the loss of the entire pair.
Updated user's guide, documentation and tests.
Renamed normalize() to normOffsets().
Added library size specification to DIList methods normOffsets(), asDGEList().
Fixed bugs under pathological settings in plotPlaid(), plotDI(), rotPlaid(), rotDI().
Optimized C++ code for connectCounts(), squareCounts().
Streamlined various R utilities used throughout all functions.
Added iter_map.py to inst/python, for iterative mapping of DNase Hi-C data.
Added the neighborCounts() function, for simultaneous read counting and enrichment calculation.
Added exclude for enrichedPairs(), to provide an exclusion zone in the local neighborhood.
Switched default colour in rotPlaid(), plotPlaid() to black.
Added compartmentalize() function to identify genomic compartments.
Added domainDirections() function to help identify domains.
Modified correctedContact() to allow distance correction and report factorized probabilities directly.
Modified marginCounts() function for proper single-end-like treatment of Hi-C data.
Extended clusterPairs() to merge bin pairs from multiple DILists.
Switched to reporting ranges directly from boxPairs(), added support for minimum bounding box output.
Modified consolidatePairs() to accept index vectors for greater modularity.
Added reference argument for large bin pairs, in filterDirect() and filterTrended().
Added filterDiag() convenience function for filtering of (near-)diagonal bin pairs.
Slight change to preparePairs() diagnostic reports when dedup=FALSE, and for unpaired reads.
Added option for a distance-based threshold to define invalid chimeras in preparePairs().
Updated documentation, tests and user's guide.
Added diffHic paper entry to CITATION.
New package diffHic, for detection of differential interactions from Hi-C data.