filterWindowsGlobal() finally behaves correctly for variable-width data=.
normFactors() and normOffsets() accept DGEList inputs in their object= and se.out= arguments.
mergeResults() and friends now default to taking tab= from the mcols() of the inputs.
Accept a list of BamFiles in bam.files= for all functions.
Removed deprecated functionality in consolidateTests() and related functions.
Modified the method used to count the number of up/down windows in combineTests(). Reported a representative test in the output along with its log-fold changes.
Renamed mixedClusters() to mixedTests() with deprecation of the former.
Added minimalTests() for cluster-level summarization with a minimum proportion of significant tests.
Standardized the output of getBestTest(), empiricalFDR(), mixedTests() and minimalTests() to that of combineTests(). In particular, getBestTest() now returns the index of its best window in the rep.test field.
Removed deprecated functionality in normOffsets(), readParam(), scaledAverage().
Added mergeResults(), overlapResults() wrapper functions to simplify getting region-level results.
Added mergeWindowsList(), findOverlapsList() functions for consolidating windows from multiple analyses. Deprecated consolidateWindows().
Added mergeResultsList(), overlapResultsList() wrapper functions to obtain consolidated region-level results. Deprecated consolidateTests(), consolidateOverlaps().
Renamed regions= to ranges= in mergeWindows() for consistency.
Added clusterWindowsList() to replace consolidateClusters().
Added filterWindowsGlobal(), filterWindowsLocal(), filterWindowsProportion() and filterWindowsControl(). Deprecated filterWindows().
Minor renaming of scaleControlInfo() arguments, added assay.data= and assay.back= arguments.
Deprecated the type= argument in normOffsets().
Removed the deprecated consolidateSizes() function.
Deprecated the use of BPPARAM= in readParam(). Added the BPPARAM= argument to all relevant functions.
Modified csawUsersGuide() to point to the workflow package.
Added normFactors() function to avoid confusion when normOffsets() returns factors.
Deprecated type="scaling" option in normOffsets().
Added calculateCPM() function for convenient calculation of (log-)CPMs.
Split up consolidateSizes() function into consolidateWindows(), consolidateTests() and consolidateOverlaps(). Deprecated consolidateSizes() itself.
Switched output of combineTests() and getBestTest() and related functions to a DataFrame.
Modified mergeWindows() behaviour with specified sign=, for dealing with nested windows of opposing sign.
Altered controlClusterFDR() to take the largest adjusted p-value threshold that yields a cluster-level FDR below target=.
Simplified detailRanges() output so that it no longer returns an arbitrary exon number.
Fully removed support for paramList objects.
Removed support for normalize(), modified default option for se.out= in normOffsets().
Removed support for paramList objects.
Added option for normOffsets() to return SummarizedExperiment objects containing normalization data.
Deprecated normalize() to avoid S4 method clashes.
Moved scaling prior to control-based filtering into a new function, scaleControlFilter(), for greater modularity.
Updated user's guide.
Added calculation of dominant directionality in combineTests(). Fixed out-of-array indexing bug in the C++ code.
Supported factor input for ids argument in combineTests(), getBestTest().
Added the empiricalFDR(), empiricalOverlaps() functions for controlling the empirical FDR.
Added the mixedClusters(), mixedOverlaps() functions for testing for mixed clusters.
Ensured that window-level FDR threshold chosen by controlClusterFDR() is not above the cluster-level FDR.
Minor fix to scaledAverage() to avoid slightly inaccurate results. Also, zero or negative scale factors now return -Inf and NA, respectively.
Switched to new scaleOffset() function for adding offsets in asDGEList(). Added option to specify the assay to be used.
Added multi-TSS support in detailRanges().
Modified paired-end machinery in windowCounts(), getPESizes() to be more accommodating of overruns.
Ignored secondary and supplementary alignments in all functions.
Added options to specify assay in SE objects in filterWindows().
Replaced weighting with normalization options in profileSites().
Updated user's guide.
Added protection against NA values in filterWindows().
Deprecated the use of parameter lists in any param= arguments.
Tightened up allowable values of ext= arguments in various functions.
Added the BPPARAM slot in the readParam class to store BiocParallelParam objects.
Added support for parallelization in windowCounts(), regionCounts() and others.
Updated documentation, user's guide.
Restored normalize() as a S4 method returning a RangedSummarizedExperiment object.
Modified asDGEList() to use any available normalization data in the input object.
Generalized S4 methods to apply on SummarizedExperiment objects.
Removed the rescue.ext option for PE handling, to maintain consistent totals calculations.
Removed the fast.pe option for PE data handling, in favour of improved default processing.
Removed dumpPE(), which is not required without the fast.pe option.
Removed makeExtVector() in favour of list/DataFrame specification.
windowCounts() and regionCounts() now compute and store the mean PE size and read length.
Minor fix in correlateReads() for end-of-chromosome behaviour.
Modified checkBimodality() so that the width argument behaves like ext in windowCounts().
extractReads() with as.reads=TRUE for PE data now returns a GRangesList.
Added the controlClusterFDR(), clusterWindows() and consolidateClusters() functions to automate control of the cluster-level FDR.
Added protection against NA values in the cluster IDs for combineTests(), getBestTest(), upweightSummits().
All read extraction methods are now CIGAR-aware and will ignore soft-clipped parts of the alignment.
Added clusterFDR() function to compute the FDR for clusters of DB windows.
Added checkBimodality() function to compute bimodality scores for regions.
Modified normalize(), asDGEList() to allow manual specification of library sizes.
Switched from normalizeCounts(), normalize() to S4 method normOffsets().
Modified default parameter specification in strandedCounts(), to avoid errors.
Switched to warning from error when a restricted chromosome is specified in extractReads().
Modified extractReads() interface with improved support for extended read and paired read extraction.
Added normalization options to filterWindows() when using control samples.
Fixed bug for proportional filtering in filterWindows().
Allowed correlateReads() to accept paired-end specification when extracting data.
Added maximizeCcf() function to estimate the average fragment length.
Added support for strand-specific overlapping in detailRanges().
Increased the fidelity of retained information in dumped BAM file from dumpPE().
Modified strand specification arguments for profileSites(), allowed reporting of individual profiles.
Removed param= specification from wwhm().
Switched to RangedSummarizedExperiment conventions for all relevant functions.
Switched to mapqFilter for scanBam() when filtering on mapping quality.
Added tests for previously untested functions.
Slight updates to documentation, user's guide.
Added getWidths(), scaledAverage() and filterWindows(), to facilitate comparison of abundances during filtering.
Added findMaxima() to identify locally maximal windows from range data.
Added profileSites() to examine the coverage profile around specified regions, with wwhm() to guess the ideal window size from the profile.
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.
Switched from the depracated rowData to rowRanges for all manipulations of SummarizedExperiment.
Changed all instances of ‘pet’ to ‘pe’ in read parameter specification, and renamed getPETSizes() to getPESizes().
Removed the redundant rescue.pairs parameter in readParam().
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.
Added support for custom column specification in getBestTest(), combineTests().
Switched from reporting average log-FC to numbers of up/down windows in combineTests().
Allowed getBestTest() to return all fields associated with the best window in the output table.
Added upweightSummits() to compute weights favouring high-abundance windows.
Added combineOverlaps(), getBestOverlaps() and summitOverlaps() wrapper functions for processing of Hits objects.
Added consolidateSizes(), to consolidate DB results from multiple window sizes.
Added support for custom key/name specification in detailRanges() for non-human/mouse systems.
Added support for strand-specific read extraction in readParam(), strand-specific counting via strandedCounts().
Added strand-awareness to mergeWindows(). Added protection against stranded input regions in extractReads(), detailRanges().
Changed algorithm for splitting of large peaks in mergeWindows().
Stored counting parameters in exptData for windowCounts(), regionCounts().
Fixed small inaccuracies with continuity correction addition in normalizeCounts() for NB-loess.
Switched to fragment midpoint for binning of paired-end data in windowCounts().
Added support for lists of library-specific readParam objects in windowCounts(), regionCounts(), correlateReads().
Added makeExtVector(), to support variable read extension lengths between libraries in windowCounts(), regionCounts().
Added support for read extension within extractReads().
Updated the user's guide to reflect new and modified functions.
Added sra2bam.sh in inst/doc to reproducibly generate BAM files to run UG examples.
Cleaned up code in inst/tests for modified functions, added new tests for new functions.
New package csaw, for de novo detection of differential binding in ChIP-seq data.