Changes in version 2.8.0 o Features • dba.report: add precision option to dba.report • dba.plot*: make plots use same precision as reports when thresholding • dba: add dir option to dba o Documentation updates • Vignette: change default to bFullLibrarySize=TRUE in description of DESeq2 analysis • Vignette: update vignette to not change dir • dba.report: clean up description of bCalled in man page • dba.report: modify example inman page to be clearer • dba: update man page to not change dir • dba.save: dontrun example code for dba.save writing into LIB • dba: dontrun example code for dba setting wd to LIB o Bug fixes • dba.report: Sort report by FDR instead of p_value • dba.peakset: fix bug when adding consensus peaks with chromosomes not present in some peaksets • dba.count: fix bug when recentering passed-in peaks • dba.report: fix bug when using filtering from dba.analyze • dba.count: fix bug when passing in peaks using factors • dba.count: fix bug caused by not registering one of the C routines correctly. Changes in version 2.6.0 o Feature changes • Change sortFun parameter in dba.plotHeatmap to default sd, with FALSE as option for no sorting • Sort peaks when adding directly via dba.peakset • don't add _ if no initString in dba.report • Internal feature: alternate peak counts: pv.resetCounts o Bug Fixes • Fix bug in dba.plotHeatmap is all values in a row are zero • Change authors in vignette to conform to new standard • Fix single peak boundary conditions • Subset config$fragmentSize when masking • Update example peaks to match data objects • Fix bug in dba.plotHeatmap if all values in a row are zero • Bugfix when returning report as GRanges with only one site • Bugfix when plotting venns of consensus peaksets • Fix buffer overrun causing segfault on MacOS Changes in version 2.4.0 o Feature: add new plot - dba.plotVolcano Changes in version 2.2.0 o Feature: Control which principal components are plotted using components parameter in dba.plotPCA o Feature: Control axis range using xrange and yrange parameters in dba.plotMA o Feature: Filtering per-contrast using filter and filterFun parameters in dba.analyze) o Feature: Flip which group in contrast shows gain/loss (sign of fold change) using bFlip parameter in dba.report o Feature: Flip which group in contrast shows gain/loss (sign of fold change) using bFlip parameter in dba.plotMA Changes in version 2.0.0 o Feature changes • Change default analysis method to DESeq2 for its more conservative normalization • Designate DESeq method as obsolete (in favor of DESeq2); alter documentation and vignette accordingly. • Change default FDR threshold to 0.05 • Add bNot parameter to dba.contrast to remove ! contrasts by default • Remove bReturnPeaksets parameter from dba.plotVenn (does this by default) • Change bCorPlot default to FALSE (no more automatic clustering heatmaps) o Internal changes • Bump version number to 2.0 • Update vignette • Remove $allvectors and $vectors; replace with $merged (without score matrix) and $binding • Upgrade peaksort to use inplace peakOrder • Optimize peak merging memory usage • Change PCA method from princomp() to prcomp() • maxGap implemented in merge • Include the beginnings of some unit tests using the testthat package. o Bug fixes • Fix bug in retrieving SummarizedExperiment • Fix bug when no peaks • Fix bugs in non-standard chromosome names and chromosome order • Fix bugs in Called logical vectors • Ensure loading sample sheet doesn't treat hash as comment char. • Tildes in file paths now accepted. • Spaces trimmed from entries in sample sheets (with warning). • Functions added to importFrom stats to satisfy BiocCheck. Changes in version 1.16.0 o Roll up bugfixes o dba.plotHeatmap returns binding sites in row order Changes in version 1.14.0 o Add support for reading Excel-format sample sheets (.xls, .xlsx extensions o Update DESeq2 reference in vignette; fix vignette samplesheet o use vennPlot from systemPiper o Fix Makevars to avoid gnu-specific extensions o Replace 'require' with 'requireNamespace' to eliminate NOTEs regarding misuse of 'require' o Remove non-ASCII characters from a couple of comments o Change Gord's email address o New: color vector lists for dba.plotHeatmap and colors for dba.plotPCA labels o Fix: bug causing two plots when changing score in dba.plotHeatmap and dba.plotPCA Changes in version 1.12.0 o Mostly bug fixes! Changes in version 1.10.0 o Counting • New: option to compute summits • New: option to center peaks with fixed width around summits • New: scores for summits (height, position) and CPM for TMM values • New: filter reads by mapping quality (mapQCth) • New: support for PE bam data using summarizeOverlaps • Remove: bCalledMask (now always TRUE) • Change: insertLength to fragmentSize • Add: fragmentSize can be a vector with a size for each sample • Change: fragmentSize default is 125 bp o Plotting • Change: colors based on CRUK color scheme • PCA plots • New: legend • New: label parameter for adding text labels of points in 2D plot • Venn diagrams • New: plot overlaps of differentially bound sites by specifying contrasts, thresholds etc. • New: able to return overlapping peaksets as GRanges directly • New: able to generate new DBA object consisting of overlapping peaks • New: labelAttributes for controlling default labels • New: default main and sub titles • Heatmaps • Fix: don’t plot column vector for attributes where every sample has a different value o General • New: add attribute value: DBA_ALL_ATTRIBUTES • Change: SN (signal/noise) to FRIP (fraction of reads in peaks) • Change: “Down” to “Loss” and Up” to “Gain” • Vignette • Change: vignette uses BiocStyles and dynamically generated figures • Change: example data based on hg19 instead of hg18 • Change: example reads from bam files instead of bed files • New: section on using DiffBind and ChIPQC together • New configuration defaults options (DBA$config): • Metadata name strings: ID, Tissue, Factor, Condition, Treatment, Caller • th: significance threshold • bUsePval • fragmentSize • mapQCth: filter reads by mapping quality • fragments (for summarizeOverlaps) o Bugs/Issues • Fix: bRemoveDuplicates had some unpredictable behaviour • Fix: chrN_random were being counted against chrN • Disable: tamoxifen_GEO.R doesn’t work after SRA changed format of archived data Changes in version 1.8.0 o Add support for DESeq2: • New: Add DBA_DESEQ2, DBA_ALL_METHODS and DBA_ALL_BLOCK method constants • Change: dba.analyze can analyze using DESeq2 • Change: all reporting and plotting functions support DESeq2 results • Change: vignette includes comparison of edgeR, DESeq, and DESeq2 o Changes to counting using dba.count: • Change: optimize built-in counting code to use much less memory and run faster • Change: deprecate bLowMem, replaced with bUseSummarizeOverlaps • New: add readFormat parameter to specify read file type (instead of using file suffix) o New: generation of result-based DBA object using dba.report (makes it easier to work with differentially bound peaksets) o Changes to defaults: • Change: default score is now DBA_SCORE_TMM_MINUS_FULL instead of DBA_SCORE_TMM_MINUS_EFFECTIVE in dba.count • Change: default value for bFullLibrarySize is now TRUE in dba.analyze • New: add bCorPlot option to DBA$config to turn off CorPlot by default o Various bugfixes, improved warnings, updated documentation Changes in version 1.6.0 o New: Low memory counting of bam files using Rsamtools and summarizeOverlaps (bLowMem in dba.count) o New: Ability to read in externally derived counts (e.g. from htSeq) (dba.count) o Improved: Features to deal with filtering intervals based on read scores (dba.count) • Change parameter name: maxFilter -> filter • Allow maxFilter to be a numerical vector to retrieve filtering rate • Add parameter: filterFun to control filtering method o New: Support for SummarizedExperiment objects (dba and dba.report) • Add bSummarizedExperiment option to dba() to convert DBA object • Add DataType = DBA_DATA_SUMMARIZED_REPORT option to dba.report() to return SummarizedExperiment o Documentation: Add section to vignette showing how to obtain full tamoxifen resistance dataset • Add section to vignette showing how to obtains full tamoxifen dataset • Add script (tamoxifen_GEO.R) and sample sheet (tamoxifen_GEO.csv) to extras for full tamoxifen dataset • Add examples to man page for dba.count to show filtering • Add examples to man pages for dba and dba.report to show retrieval of SummarizedExperiment objects • Update and cleanup vignette and man pages o Various bugfixes and improved warnings Changes in version 1.4.0 o Plotting • dba.plotMA • Smooth plots now default • Added fold parameter in addition to th (threshold) • dba.plotHeatmap • Side colorbars added • Add support for specifying sample mask to include any subset of samples in a contrast plot, including samples that were not in the original contrast • dba.plotVenn • Changed plotter from limma to T. Girke's overLapper • Added support for 4-way Venns (also in dba/overlap) • dba.plotPCA • Add support for specifying sample mask to include any subset of samples in a contrast plot, including samples that were not in the original contrast o Peaksets (dba and dba.peakset) • Peakset formats • narrowPeaks format supported • Can override file format, score column, and score orientation defaults for supported peak callers • Consensus peaksets • Added ability to generate sets of consensus peaksets based on metadata attributes: for example create consensus peaksets for each tissue type and/or condition, or for all unique samples by taking the consensus of their replicate peaksets o Read counting (dba.count) • Compute Signal-to-Noise ratio when counting • Added bScaleControl to down-scale control reads by default • Add option to specify a mask in peak parameter to limit which peaksets are used to for a consensus by overlap. Works with new consensus peakset options in dba.peakset • Remove references to support for SAM files o Analysis (dba.analyze) • edgeR: updated calls to math change sin edgeR; updated vignette and references • DESeq: updated to work with current DESeq; use pooled-CR dispersion estimation method for blocking analysis; update vignette o Various bug fixes; more informative warnings; update documentation including vignette, new examples and cross-referencing in man pages Changes in version 1.2.0 (2012-03-30) o GRanges is default class for peaksets and reports instead of RangedData, controlled by DataType parameter. o Both analysis methods (edgeR and DESeq) use generalized linear models (GLMs) for two-group contrasts by default. o Blocking factors (for two-factor analysis) can be specified flexibly such that arbitrary blocking factors can be used. o Section added to vignette showing an analysis using a blocking factor. o Added new metadata type, DBA_TREATMENT. o New DBA_SCORE_ options for specifying scoring method, including TMM normalized counts, and ability to change scoring method on the fly in dba.plotHeatmap and dba.plotPCA when plotting global binding matrix. o bRemoveDuplicates parameter in dba.count allows duplicate reads to be discarded when computing counts o More efficient use of memory when analyzing (controlled by bReduceObjects parameter in dba.analyze). o various bugs fixed, man pages updated, and warning messages added. Changes in version 1.0.0 o Initial release