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