1. chromstaR
  2. NEWS
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version bump to 1.21.1

ataudt authored on 29/10/2021 07:39:46
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NEWS
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+CHANGES IN VERSION 1.21.1
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+-------------------------
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+BUG FIXES
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+    o Fixed ENSEMBL host for rnorvegicus_gene_ensembl. Using default host now instead of may2012.archive.ensembl.org.
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 CHANGES IN VERSION 1.14.2
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Browse code

added bugfix to NEWS

ataudt authored on 23/10/2020 18:04:59
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NEWS
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+CHANGES IN VERSION 1.14.2
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+-------------------------
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+BUG FIXES
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+    o Corrected format check for experiment.table: Spaces are not excepted any longer, because they lead to downstream errors.
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Browse code

updated NEWS

ataudt authored on 29/04/2020 22:17:45
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NEWS
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+CHANGES IN VERSION 1.14.1
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+-------------------------
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+BUG FIXES
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+    o Compatibility update: Replaced class() checks with is().
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 CHANGES IN VERSION 1.13.1
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Browse code

version change to 1.13.1

ataudt authored on 18/04/2020 18:28:35
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NEWS
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-CHANGES IN VERSION 1.13.2
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+CHANGES IN VERSION 1.13.1
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 BUG FIXES
Browse code

bugfix fetchExtendenChromInfoFromUCSC -> getChromInfoFromUCSC

ataudt authored on 11/04/2020 18:36:05
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NEWS
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+CHANGES IN VERSION 1.13.2
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+-------------------------
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+BUG FIXES
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+    o Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC().
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 CHANGES IN VERSION 1.11.1
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Browse code

bugfix for export empty univariate peaks

ataudt authored on 27/05/2019 08:49:37
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NEWS
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+CHANGES IN VERSION 1.11.1
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+-------------------------
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+BUGFIXES
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+    o Bugfix for error when exporting empty peaks in univariateHMM.
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Browse code

version bump to 1.9.2

ataudt authored on 18/02/2019 19:15:08
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NEWS
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+CHANGES IN VERSION 1.9.2
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+------------------------
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+BUGFIXES
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+    o Bugfix for error when exporting empty peak lists.
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Browse code

bugfixes in version 1.7.2

ataudt authored on 14/07/2018 13:39:28
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NEWS
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+CHANGES IN VERSION 1.7.2
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+------------------------
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+BUGFIXES
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+    o Compatibility fixes for the new release of ggplot2 (3.0.0).
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+    o seqlevels() that are smaller than binsize are dropped properly in fixedWidthBins() and variableWidthBins().
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Browse code

changePostCutoff works for univariate peak calls without keep.posteriors=TRUE

ataudt authored on 18/04/2018 08:41:49
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NEWS
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+CHANGES IN VERSION 1.5.3
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+------------------------
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+SIGNIFICANT USER-LEVEL CHANGES
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+    o Function 'changePostCutoff()' works on univariate peak calls without posterior needing to be present.
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Browse code

renamed adjustSensitivity to changeMaxPostCutoff

chakalakka authored on 15/02/2018 10:05:19
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NEWS
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     o Score in exported BED files is calculated as -10*log10(maxPostInPeak).
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-    o 'changeFDR()' was renamed to 'adjustSensitivity()'.
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+    o 'changeFDR()' was renamed to 'changeMaxPostCutoff()'.
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 CHANGES IN VERSION 1.3.1
Browse code

added maxPostInPeak

chakalakka authored on 14/02/2018 09:14:58
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NEWS
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-    o Column 'peakScores' is now bounded between 0 and 1000 and approximately uniformly distributed.
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+    o New column 'maxPostInPeak' containing the maximum posterior within each peak.
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+    o Score in exported BED files is calculated as -10*log10(maxPostInPeak).
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     o 'changeFDR()' was renamed to 'adjustSensitivity()'.
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Browse code

updated news

chakalakka authored on 31/01/2018 15:27:31
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NEWS
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-CHANGES IN VERSION 1.3.2
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+CHANGES IN VERSION 1.5.1
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Browse code

updated vignette

chakalakka authored on 24/11/2017 15:18:28
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NEWS
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-    o Column 'peakScores' is now bounded between 0 and 1000 and uniformly distributed. It is calculated from columns 'posteriorScores'.
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+    o Column 'peakScores' is now bounded between 0 and 1000 and approximately uniformly distributed.
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+    o 'changeFDR()' was renamed to 'adjustSensitivity()'.
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Browse code

changed NEWS

chakalakka authored on 19/10/2017 13:34:29
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NEWS
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-    o Column 'peakScores' is now bounded between 0 and 1000. It is calculated from columns 'posteriorScores'.
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+    o Column 'peakScores' is now bounded between 0 and 1000 and uniformly distributed. It is calculated from columns 'posteriorScores'.
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 CHANGES IN VERSION 1.3.1
Browse code

added linearized posteriorScores

chakalakka authored on 20/07/2017 09:26:25
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NEWS
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+CHANGES IN VERSION 1.3.2
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+------------------------
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+SIGNIFICANT USER-LEVEL CHANGES
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+    o Column 'peakScores' is now bounded between 0 and 1000. It is calculated from columns 'posteriorScores'.
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Browse code

use stepsize counts instead of averaged ones

chakalakka authored on 08/05/2017 07:24:22
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NEWS
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-    o New default value for Chromstar(..., stepsize = 1/5 * binsize).
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+    o New default value for Chromstar(..., stepsize = 1/2 * binsize).
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 CHANGES IN VERSION 1.1.4
Browse code

version bump to 1.3.1

chakalakka authored on 05/05/2017 14:51:41
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NEWS
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-CHANGES IN VERSION 1.1.5
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+CHANGES IN VERSION 1.3.1
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 NEW FEATURES
Browse code

implemented sliding bins with stepsize

chakalakka authored on 07/04/2017 17:16:43
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+CHANGES IN VERSION 1.1.5
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+------------------------
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+NEW FEATURES
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+    o New parameter 'stepsize' allows sliding bins. This improves localization of peaks.
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+SIGNIFICANT USER-LEVEL CHANGES
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+    o New default value for Chromstar(..., stepsize = 1/5 * binsize).
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     o Fixed a mistake in the calculation of differential scores from version 1.1.2
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 CHANGES IN VERSION 1.1.2
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Browse code

fixed bug in scores

chakalakka authored on 13/02/2017 10:08:45
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-CHANGES IN VERSION 1.1.3
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+CHANGES IN VERSION 1.1.4
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Browse code

fixed mistake in differential scores

chakalakka authored on 06/02/2017 12:26:07
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NEWS
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+CHANGES IN VERSION 1.1.3
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+------------------------
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+BUG FIXES
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+    o Fixed a mistake in the calculation of differential scores from version 1.1.2
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-    o Fixed a bug where chromosomes with a single bin where making problems.
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+    o Fixed a bug where chromosomes with a single bin were making problems.
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 CHANGES IN VERSION 1.1.1
Browse code

updated NEWS

chakalakka authored on 03/02/2017 13:34:57
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NEWS
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     o Proper print() methods for all objects.
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+BUG FIXES
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+    o Fixed a bug where chromosomes with a single bin where making problems.
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Browse code

bumped version to 1.1.2

chakalakka authored on 02/02/2017 15:49:02
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NEWS
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+CHANGES IN VERSION 1.1.2
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+------------------------
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+NEW FEATURES
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+    o Proper print() methods for all objects.
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bugfix in mergeChroms for only one chromosome

chakalakka authored on 19/10/2016 13:03:32
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+CHANGES IN VERSION 1.1.1
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+------------------------
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+NEW FEATURES
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+    o Selection of peaks can be done with 'changeFDR'.
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+    o Peak calls are available in each chromstaR-object as list entry '$peaks'.
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+SIGNIFICANT USER-LEVEL CHANGES
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+    o 'plotFoldEnrichment' renamed to 'plotEnrichment'.
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+    o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates' replaced by 'exportCounts', 'exportPeaks', 'exportCombinations'.
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+BUG FIXES
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+    o Proper computation of fold enrichments, with < 1 indicating depletion and > 1 indicating enrichment.
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+DEPRECATED AND DEFUNCT
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+    o 'changePostCutoff'.
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+    o 'plotFoldEnrichment'.
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+    o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates'.