Changes in version 1.6.1: o Fix to track change in edgeR interface 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