Changes in version 1.11.4:
o Removed support for paramList objects.
o Added option for normOffsets() to return SummarizedExperiment
objects containing normalization data.
o Deprecated normalize() to avoid S4 method clashes.
o Moved scaling prior to control-based filtering into a new function,
scaleControlFilter(), for greater modularity.
o Updated user's guide.
Changes in version 1.10.0:
o Added calculation of dominant directionality in combineTests().
Fixed out-of-array indexing bug in the C++ code.
o Supported factor input for ids argument in combineTests(),
getBestTest().
o Added the empiricalFDR(), empiricalOverlaps() functions for
controlling the empirical FDR.
o Added the mixedClusters(), mixedOverlaps() functions for testing for
mixed clusters.
o Ensured that window-level FDR threshold chosen by
controlClusterFDR() is not above the cluster-level FDR.
o Minor fix to scaledAverage() to avoid slightly inaccurate results.
Also, zero or negative scale factors now return -Inf and NA,
respectively.
o Switched to new scaleOffset() function for adding offsets in
asDGEList(). Added option to specify the assay to be used.
o Added multi-TSS support in detailRanges().
o Modified paired-end machinery in windowCounts(), getPESizes() to be
more accommodating of overruns.
o Ignored secondary and supplementary alignments in all functions.
o Added options to specify assay in SE objects in filterWindows().
o Replaced weighting with normalization options in profileSites().
o Updated user's guide.
Changes in version 1.8.0:
o Added protection against NA values in filterWindows().
o Deprecated the use of parameter lists in any param= arguments.
o Tightened up allowable values of ext= arguments in various
functions.
o Added the BPPARAM slot in the readParam class to store
BiocParallelParam objects.
o Added support for parallelization in windowCounts(), regionCounts()
and others.
o Updated documentation, user's guide.
Changes in version 1.6.0:
o Restored normalize() as a S4 method returning a
RangedSummarizedExperiment object.
o Modified asDGEList() to use any available normalization data in the
input object.
o Generalized S4 methods to apply on SummarizedExperiment objects.
o Removed the rescue.ext option for PE handling, to maintain
consistent totals calculations.
o Removed the fast.pe option for PE data handling, in favour of
improved default processing.
o Removed dumpPE(), which is not required without the fast.pe option.
o Removed makeExtVector() in favour of list/DataFrame specification.
o windowCounts() and regionCounts() now compute and store the mean PE
size and read length.
o Minor fix in correlateReads() for end-of-chromosome behaviour.
o Modified checkBimodality() so that the width argument behaves like
ext in windowCounts().
o extractReads() with as.reads=TRUE for PE data now returns a
GRangesList.
o Added the controlClusterFDR(), clusterWindows() and
consolidateClusters() functions to automate control of the
cluster-level FDR.
o Added protection against NA values in the cluster IDs for
combineTests(), getBestTest(), upweightSummits().
o All read extraction methods are now CIGAR-aware and will ignore
soft-clipped parts of the alignment.
Changes in version 1.4.0:
o Added clusterFDR() function to compute the FDR for clusters of DB
windows.
o Added checkBimodality() function to compute bimodality scores for
regions.
o Modified normalize(), asDGEList() to allow manual specification of
library sizes.
o Switched from normalizeCounts(), normalize() to S4 method
normOffsets().
o Modified default parameter specification in strandedCounts(), to
avoid errors.
o Switched to warning from error when a restricted chromosome is
specified in extractReads().
o Modified extractReads() interface with improved support for extended
read and paired read extraction.
o Added normalization options to filterWindows() when using control
samples.
o Fixed bug for proportional filtering in filterWindows().
o Allowed correlateReads() to accept paired-end specification when
extracting data.
o Added maximizeCcf() function to estimate the average fragment
length.
o Added support for strand-specific overlapping in detailRanges().
o Increased the fidelity of retained information in dumped BAM file
from dumpPE().
o Modified strand specification arguments for profileSites(), allowed
reporting of individual profiles.
o Removed param= specification from wwhm().
o Switched to RangedSummarizedExperiment conventions for all relevant
functions.
o Switched to mapqFilter for scanBam() when filtering on mapping
quality.
o Added tests for previously untested functions.
o Slight updates to documentation, user's guide.
Changes in version 1.2.0:
o Added getWidths(), scaledAverage() and filterWindows(), to
facilitate comparison of abundances during filtering.
o Added findMaxima() to identify locally maximal windows from range
data.
o Added profileSites() to examine the coverage profile around
specified regions, with wwhm() to guess the ideal window size from
the profile.
o Changed default window width in windowCounts() to 50 bp, default
filter to a fixed count of 10. Also, filter=0 is honored when
bin=TRUE.
o Switched from the depracated rowData to rowRanges for all
manipulations of SummarizedExperiment.
o Changed all instances of `pet' to `pe' in read parameter
specification, and renamed getPETSizes() to getPESizes().
o Removed the redundant rescue.pairs parameter in readParam().
o Added fast.pe parameter in readParam(), for fast paired-end data
extraction. Added dumpPE() to pre-process paired-end BAM files for
fast downstream extraction.
o Added support for custom column specification in getBestTest(),
combineTests().
o Switched from reporting average log-FC to numbers of up/down windows
in combineTests().
o Allowed getBestTest() to return all fields associated with the best
window in the output table.
o Added upweightSummits() to compute weights favouring high-abundance
windows.
o Added combineOverlaps(), getBestOverlaps() and summitOverlaps()
wrapper functions for processing of Hits objects.
o Added consolidateSizes(), to consolidate DB results from multiple
window sizes.
o Added support for custom key/name specification in detailRanges()
for non-human/mouse systems.
o Added support for strand-specific read extraction in readParam(),
strand-specific counting via strandedCounts().
o Added strand-awareness to mergeWindows(). Added protection against
stranded input regions in extractReads(), detailRanges().
o Changed algorithm for splitting of large peaks in mergeWindows().
o Stored counting parameters in exptData for windowCounts(),
regionCounts().
o Fixed small inaccuracies with continuity correction addition in
normalizeCounts() for NB-loess.
o Switched to fragment midpoint for binning of paired-end data in
windowCounts().
o Added support for lists of library-specific readParam objects in
windowCounts(), regionCounts(), correlateReads().
o Added makeExtVector(), to support variable read extension lengths
between libraries in windowCounts(), regionCounts().
o Added support for read extension within extractReads().
o Updated the user's guide to reflect new and modified functions.
o Added sra2bam.sh in inst/doc to reproducibly generate BAM files to
run UG examples.
o Cleaned up code in inst/tests for modified functions, added new
tests for new functions.
Changes in version 1.0.0:
o New package csaw, for de novo detection of differential binding in
ChIP-seq data.