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NEWS
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CHANGES IN VERSION 1.27.1
-------------------------
SIGNIFICANT USER-LEVEL CHANGES
o Removed parameter "classes" from clusterHMMs(). This is due to a missing dependency (the ReorderCluster package). Sorry!
o Removed parameter "reorder.by.class" from heatmapGenomewide(). This is due to a missing dependency (the ReorderCluster package). Sorry!
CHANGES IN VERSION 1.15.2
-------------------------
BUG FIXES
o Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC().
CHANGES IN VERSION 1.12.1
-------------------------
BUG FIXES
o Moved ggplot2 from Imports to Depends. This was necessary because cowplot doesn't call ggplot2 explicitly anymore.
CHANGES IN VERSION 1.11.1
-------------------------
BUG FIXES
o Fixed "object 'dfplot.seg' not found" bug when building vignette.
CHANGES IN VERSION 1.7.2
------------------------
NEW FEATURES
o New method 'edivisive' available.
o Breakpoint detection available for both Aneufinder(..., strandseq=TRUE) and Aneufinder(..., strandseq=FALSE)
o A stepsize for a sliding window can be selected in addition to the binsize for method "HMM". This improves resolution of detected breakpoints.
o Breakpoints for Aneufinder(..., strandseq=TRUE) are reported with confidence intervals in folder BROWSERFILES.
o Breakpoint detection for Aneufinder(..., strandseq=TRUE) has an additional breakpoint refinement step which improves localization of breakpoints.
SIGNIFICANT USER-LEVEL CHANGES
o Reorganized output folder structure and added README.txt
o Renamed parameter "plot.SCE" to "plot.breakpoints".
o GC correction is now done with a loess-fit by default instead of the quadratic fit. This should improve accuracy.
o Default epsilon is now 'eps=0.01' (was 'eps=0.1' before) for method "HMM".
CHANGES IN VERSION 1.5.1
------------------------
BUG FIXES
o Can use BSgenome*NCBI* for GC correction (worked only for BSgenome*UCSC* before).
o Bugfix in bam2GRanges(..., pairedEndReads=TRUE) if both alignments are not on the same chromosome.
CHANGES IN VERSION 1.3.4
------------------------
NEW FEATURES
o Proper print() methods for AneuFinder objects.
o plotProfile(..., normalize.counts='2-somy') option added for plotting of normalized counts.
o heatmapGenomewideCluster() added for convenient assessment of the clusterByQuality() result.
BUG FIXES
o Fixed option Aneufinder(..., strandseq = TRUE) for DNAcopy method.
o Fixed a bug for SCE plotting in heatmapGenomewide().
o Proper creation of variable-width bins for huge reference files.
o Better heatmap dimensions for few cells.
o Bugfix for Inf values in clusterByQuality().
SIGNIFICANT USER-LEVEL CHANGES
o Renamed plotPCA() to plot_pca() to avoid namespace conflict with BiocGenerics.
CHANGES IN VERSION 1.3.3
------------------------
NEW FEATURES
o New function plotPCA() to do principal component analysis.
o Introduced parameter 'exclude.regions' to karyotypeMeasures(), plotHeterogeneity() and heatmapGenomewide(). This should facilitate excluding artifact regions from the clustering and karyotype measures.
o Parameter 'regions' now also available in plotHeterogeneity() (only in karyotypeMeasures() before).
SIGNIFICANT USER-LEVEL CHANGES
o The method to compute the dendrogram in heatmapGenomewide() was changed to simple hierarchical clustering on the copy number at bin-level (was segment-level before).
CHANGES IN VERSION 1.3.1
------------------------
NEW FEATURES
o Parameter 'normalChromosomeNumbers' in karyotypeMeasures() can handle mixture samples now.
CHANGES IN VERSION 1.1.6
------------------------
NEW FEATURES
o Added DNAcopy algorithm to Strand-seq mode.
SIGNIFICANT USER-LEVEL CHANGES
o Renamed parameter 'most.frequent.state.bivariate' -> 'most.frequent.state.strandseq' in Aneufinder().
o Renamed parameter 'most.frequent.state.univariate' -> 'most.frequent.state' in Aneufinder().
o New parameter 'strandseq' in Aneufinder().
BUG FIXES
o Dendrogram and heatmap are now aligned properly in heatmapGenomewide().
CHANGES IN VERSION 1.1.5
------------------------
NEW FEATURES
o Aneufinder runs DNAcopy algorithm in addition to the Hidden Markov Model.
o New function "getQC" to get a data.frame with quality metrics.
SIGNIFICANT USER-LEVEL CHANGES
o Changed folder structure to include DNAcopy method.
o Renamed methods from c('univariate','bivariate') to c('HMM','biHMM')
CHANGES IN VERSION 1.1.4
------------------------
NEW FEATURES
o karyotypeMeasures() has new option regions.
o plotHeterogeneity() for easy plotting of karyotype measures.
o BiocStyle vignette.
o New option use.bamsignals=FALSE/TRUE available for the binning step.
o getQC() handles NULL entries as NA and is thus more robust.
o complexity estimation via Michaelis-Menten is carried along.
SIGNIFICANT USER-LEVEL CHANGES
o Color scheme for copy number states has been improved for states >= 5-somy.
o Option format has been removed in all functions. File format is determined
automatically now.
o clusterByQuality() clusters now on complexity as well by default.
BUG FIXES
o Corrected bug in order of seqlevels after as(..., 'GRanges').
o Corrected bug in hotspotter() that caused detection of low-abundance hotspots.