CHANGES IN VERSION 1.21.1 ------------------------- BUG FIXES o Fixed ENSEMBL host for rnorvegicus_gene_ensembl. Using default host now instead of may2012.archive.ensembl.org. CHANGES IN VERSION 1.14.2 ------------------------- BUG FIXES o Corrected format check for experiment.table: Spaces are not excepted any longer, because they lead to downstream errors. CHANGES IN VERSION 1.14.1 ------------------------- BUG FIXES o Compatibility update: Replaced class() checks with is(). CHANGES IN VERSION 1.13.1 ------------------------- BUG FIXES o Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC(). CHANGES IN VERSION 1.11.1 ------------------------- BUGFIXES o Bugfix for error when exporting empty peaks in univariateHMM. CHANGES IN VERSION 1.9.2 ------------------------ BUGFIXES o Bugfix for error when exporting empty peak lists. CHANGES IN VERSION 1.7.2 ------------------------ BUGFIXES o Compatibility fixes for the new release of ggplot2 (3.0.0). o seqlevels() that are smaller than binsize are dropped properly in fixedWidthBins() and variableWidthBins(). CHANGES IN VERSION 1.5.3 ------------------------ SIGNIFICANT USER-LEVEL CHANGES o Function 'changePostCutoff()' works on univariate peak calls without posterior needing to be present. CHANGES IN VERSION 1.5.1 ------------------------ SIGNIFICANT USER-LEVEL CHANGES o New column 'maxPostInPeak' containing the maximum posterior within each peak. o Score in exported BED files is calculated as -10*log10(maxPostInPeak). o 'changeFDR()' was renamed to 'changeMaxPostCutoff()'. CHANGES IN VERSION 1.3.1 ------------------------ NEW FEATURES o New parameter 'stepsize' allows sliding bins. This improves localization of peaks. SIGNIFICANT USER-LEVEL CHANGES o New default value for Chromstar(..., stepsize = 1/2 * binsize). CHANGES IN VERSION 1.1.4 ------------------------ BUG FIXES o Fixed a mistake in the calculation of differential scores from version 1.1.2 CHANGES IN VERSION 1.1.2 ------------------------ NEW FEATURES o Proper print() methods for all objects. BUG FIXES o Fixed a bug where chromosomes with a single bin were making problems. CHANGES IN VERSION 1.1.1 ------------------------ NEW FEATURES o Selection of peaks can be done with 'changeFDR'. o Peak calls are available in each chromstaR-object as list entry '$peaks'. SIGNIFICANT USER-LEVEL CHANGES o 'plotFoldEnrichment' renamed to 'plotEnrichment'. o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates' replaced by 'exportCounts', 'exportPeaks', 'exportCombinations'. BUG FIXES o Proper computation of fold enrichments, with < 1 indicating depletion and > 1 indicating enrichment. DEPRECATED AND DEFUNCT o 'changePostCutoff'. o 'plotFoldEnrichment'. o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates'.