Changes in version 1.8.4: o Fix: more consistent scores for DBA_SCORE_TMM_*. o Fix: remove spurious f's in man page for dba detailing column name lables in samplesheet. o Change: disable tamoxifen_GEO.R script as it no longer works due to SRA changing data format. Changes in version 1.8.3: o Fix: bug when generating GRanges overlaps and one peakset is empty. Changes in version 1.8.2: o Fix: missing header file introduced in 1.8.1. Changes in version 1.8.1: o Fix: longstanding bug in dba.count that could cause reads mapped to chrN_random to be counted aginst intervals on chrN. 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 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