Changes in version 1.14.0
o Added the readMTX2IntSet() function to create InteractionSets
from file.
Changes in version 1.12.0
o Extended prunePairs() to acknowledge restrict, discard and cap
in param= argument.
o Extended getPairs() to acknowledge restrict, discard and cap in
param= argument.
o Added restrict.regions= option to connectCounts(),
squareCounts().
o Removed unnecessary normalize() export.
o Upgraded presplit_map.py, iter_map.py to run on Python 3 and to
use Bio.SeqIO.parse().
Changes in version 1.10.0
o Added extractPatch() function to count bin pairs in a specified
area of the interaction space.
o 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.
o Modified preparePairs() to be more generous when considering
inward-facing reads if they overlap past each other.
o Fixed bug in savePairs() involving failure to swap other
information when enforcing index ordering.
o Added mergeCMs() function to allow entry into the pipeline from
ContactMatrix objects.
o Moved pre-processing scripts out of the package to the
repository for the user's guide.
o Updated presplit_map.py to use new samtools API for sorting.
o Updated user's guide.
Changes in version 1.8.0
o Streamlined filterDirect(), filterTrended(), and added tests
for them. Also allowed specification of which assay to use for
the data and reference objects.
o enrichedPairs() and neighborCounts() now return counts for
neighbourhood regions, not just the enrichment values.
o filterPeaks() will compute (and optionally return) enrichment
values from neighbourhood counts.
o normalizeCNV() and correctedContact() allow specification of
which assay matrix to use from the SE objects.
o Refactored a great deal of the C++ code for improved clarity.
o 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.
o Updated user's guide.
Changes in version 1.6.0
o Relaxed checks in preparePairs(), prepPseudoPairs() when more
chromosomes are supplied than needed.
o Relaxed checks in connectCounts() when extra chromosomes are in
the input ranges.
o Fixed an issue with preparePairs() when too many file handles
are open.
o Fixed clash between BiocGenerics and Matrix which().
o Modified domainDirections() to return a
RangedSummarizedExperiment.
o Removed defunct DIList class and methods.
o Switched from seqlevels() to seqlevelsInUse() for fragment
intervals.
o Updated user's guide, documentation.
Changes in version 1.4.0
o
Deprecated DIList objects and methods in favour of
InteractionSet objects.
o
marginCounts() now returns a RangedSummarizedExperiment for all
bins.
o
Added the max.height argument to the rotPlaid() and rotDI()
functions.
o
Added the diClusters() function for post-hoc cluster-level FDR
control.
o
Added the annotatePairs() function for convenient annotation of
(clusters of) interactions.
o
Fixed a bug in plotPlaid() when the interaction space was
empty.
o
Fixed a bug in preparePairs() where unmapped chimeric segments
led to the loss of the entire pair.
o
Updated user's guide, documentation and tests.
Changes in version 1.2.0
o
Renamed normalize() to normOffsets().
o
Added library size specification to DIList methods
normOffsets(), asDGEList().
o
Fixed bugs under pathological settings in plotPlaid(),
plotDI(), rotPlaid(), rotDI().
o
Optimized C++ code for connectCounts(), squareCounts().
o
Streamlined various R utilities used throughout all functions.
o
Added iter_map.py to inst/python, for iterative mapping of
DNase Hi-C data.
o
Added the neighborCounts() function, for simultaneous read
counting and enrichment calculation.
o
Added exclude for enrichedPairs(), to provide an exclusion zone
in the local neighborhood.
o
Switched default colour in rotPlaid(), plotPlaid() to black.
o
Added compartmentalize() function to identify genomic
compartments.
o
Added domainDirections() function to help identify domains.
o
Modified correctedContact() to allow distance correction and
report factorized probabilities directly.
o
Modified marginCounts() function for proper single-end-like
treatment of Hi-C data.
o
Extended clusterPairs() to merge bin pairs from multiple
DILists.
o
Switched to reporting ranges directly from boxPairs(), added
support for minimum bounding box output.
o
Modified consolidatePairs() to accept index vectors for greater
modularity.
o
Added reference argument for large bin pairs, in filterDirect()
and filterTrended().
o
Added filterDiag() convenience function for filtering of
(near-)diagonal bin pairs.
o
Slight change to preparePairs() diagnostic reports when
dedup=FALSE, and for unpaired reads.
o
Added option for a distance-based threshold to define invalid
chimeras in preparePairs().
o
Updated documentation, tests and user's guide.
o
Added diffHic paper entry to CITATION.
Changes in version 1.0.0
o
New package diffHic, for detection of differential interactions
from Hi-C data.