NEWS

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chromstaR 1.21.1

BUG FIXES

• Fixed ENSEMBL host for rnorvegicus_gene_ensembl. Using default host now instead of may2012.archive.ensembl.org.

chromstaR 1.14.2

BUG FIXES

• Corrected format check for experiment.table: Spaces are not excepted any longer, because they lead to downstream errors.

chromstaR 1.14.1

BUG FIXES

• Compatibility update: Replaced class() checks with is().

chromstaR 1.13.1

BUG FIXES

• Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC().

chromstaR 1.11.1

BUGFIXES

• Bugfix for error when exporting empty peaks in univariateHMM.

chromstaR 1.9.2

BUGFIXES

• Bugfix for error when exporting empty peak lists.

chromstaR 1.7.2

BUGFIXES

• Compatibility fixes for the new release of ggplot2 (3.0.0).
• seqlevels() that are smaller than binsize are dropped properly in fixedWidthBins() and variableWidthBins().

chromstaR 1.5.3

SIGNIFICANT USER-LEVEL CHANGES

• Function 'changePostCutoff()' works on univariate peak calls without posterior needing to be present.

chromstaR 1.5.1

SIGNIFICANT USER-LEVEL CHANGES

• New column 'maxPostInPeak' containing the maximum posterior within each peak.
• Score in exported BED files is calculated as -10*log10(maxPostInPeak).
• 'changeFDR()' was renamed to 'changeMaxPostCutoff()'.

chromstaR 1.3.1

NEW FEATURES

• New parameter 'stepsize' allows sliding bins. This improves localization of peaks.

SIGNIFICANT USER-LEVEL CHANGES

• New default value for Chromstar(..., stepsize = 1/2 * binsize).

chromstaR 1.1.4

BUG FIXES

• Fixed a mistake in the calculation of differential scores from version 1.1.2

chromstaR 1.1.2

NEW FEATURES

• Proper print() methods for all objects.

BUG FIXES

• Fixed a bug where chromosomes with a single bin were making problems.

chromstaR 1.1.1

NEW FEATURES

• Selection of peaks can be done with 'changeFDR'.
• Peak calls are available in each chromstaR-object as list entry '$peaks'.

SIGNIFICANT USER-LEVEL CHANGES

• 'plotFoldEnrichment' renamed to 'plotEnrichment'.
• 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates' replaced by 'exportCounts', 'exportPeaks', 'exportCombinations'.

BUG FIXES

• Proper computation of fold enrichments, with < 1 indicating depletion and > 1 indicating enrichment.

DEPRECATED AND DEFUNCT

• 'changePostCutoff'.
• 'plotFoldEnrichment'.
• 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates'.