NEWS

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AneuFinder 1.27.1

SIGNIFICANT USER-LEVEL CHANGES

• Removed parameter "classes" from clusterHMMs(). This is due to a missing dependency (the ReorderCluster package). Sorry!
• Removed parameter "reorder.by.class" from heatmapGenomewide(). This is due to a missing dependency (the ReorderCluster package). Sorry!

AneuFinder 1.15.2

BUG FIXES

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

AneuFinder 1.12.1

BUG FIXES

• Moved ggplot2 from Imports to Depends. This was necessary because cowplot doesn't call ggplot2 explicitly anymore.

AneuFinder 1.11.1

BUG FIXES

• Fixed "object 'dfplot.seg' not found" bug when building vignette.

AneuFinder 1.7.2

NEW FEATURES

• New method 'edivisive' available.
• Breakpoint detection available for both Aneufinder(..., strandseq=TRUE) and Aneufinder(..., strandseq=FALSE)
• A stepsize for a sliding window can be selected in addition to the binsize for method "HMM". This improves resolution of detected breakpoints.
• Breakpoints for Aneufinder(..., strandseq=TRUE) are reported with confidence intervals in folder BROWSERFILES.
• Breakpoint detection for Aneufinder(..., strandseq=TRUE) has an additional breakpoint refinement step which improves localization of breakpoints.

SIGNIFICANT USER-LEVEL CHANGES

• Reorganized output folder structure and added README.txt
• Renamed parameter "plot.SCE" to "plot.breakpoints".
• GC correction is now done with a loess-fit by default instead of the quadratic fit. This should improve accuracy.
• Default epsilon is now 'eps=0.01' (was 'eps=0.1' before) for method "HMM".

AneuFinder 1.5.1

BUG FIXES

• Can use BSgenome*NCBI* for GC correction (worked only for BSgenome*UCSC* before).
• Bugfix in bam2GRanges(..., pairedEndReads=TRUE) if both alignments are not on the same chromosome.

AneuFinder 1.3.4

NEW FEATURES

• Proper print() methods for AneuFinder objects.
• plotProfile(..., normalize.counts='2-somy') option added for plotting of normalized counts.
• heatmapGenomewideCluster() added for convenient assessment of the clusterByQuality() result.

BUG FIXES

• Fixed option Aneufinder(..., strandseq = TRUE) for DNAcopy method.
• Fixed a bug for SCE plotting in heatmapGenomewide().
• Proper creation of variable-width bins for huge reference files.
• Better heatmap dimensions for few cells.
• Bugfix for Inf values in clusterByQuality().

SIGNIFICANT USER-LEVEL CHANGES

• Renamed plotPCA() to plot_pca() to avoid namespace conflict with BiocGenerics.

AneuFinder 1.3.3

NEW FEATURES

• New function plotPCA() to do principal component analysis.
• Introduced parameter 'exclude.regions' to karyotypeMeasures(), plotHeterogeneity() and heatmapGenomewide(). This should facilitate excluding artifact regions from the clustering and karyotype measures.
• Parameter 'regions' now also available in plotHeterogeneity() (only in karyotypeMeasures() before).

SIGNIFICANT USER-LEVEL CHANGES

• 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).

AneuFinder 1.3.1

NEW FEATURES

• Parameter 'normalChromosomeNumbers' in karyotypeMeasures() can handle mixture samples now.

AneuFinder 1.1.6

NEW FEATURES

• Added DNAcopy algorithm to Strand-seq mode.

SIGNIFICANT USER-LEVEL CHANGES

• Renamed parameter 'most.frequent.state.bivariate' -> 'most.frequent.state.strandseq' in Aneufinder().
• Renamed parameter 'most.frequent.state.univariate' -> 'most.frequent.state' in Aneufinder().
• New parameter 'strandseq' in Aneufinder().

BUG FIXES

• Dendrogram and heatmap are now aligned properly in heatmapGenomewide().

AneuFinder 1.1.5

NEW FEATURES

• Aneufinder runs DNAcopy algorithm in addition to the Hidden Markov Model.
• New function "getQC" to get a data.frame with quality metrics.

SIGNIFICANT USER-LEVEL CHANGES

• Changed folder structure to include DNAcopy method.
• Renamed methods from c('univariate','bivariate') to c('HMM','biHMM')

AneuFinder 1.1.4

NEW FEATURES

• karyotypeMeasures() has new option regions.
• plotHeterogeneity() for easy plotting of karyotype measures.
• BiocStyle vignette.
• New option use.bamsignals=FALSE/TRUE available for the binning step.
• getQC() handles NULL entries as NA and is thus more robust.
• complexity estimation via Michaelis-Menten is carried along.

SIGNIFICANT USER-LEVEL CHANGES

• Color scheme for copy number states has been improved for states >= 5-somy.
• Option format has been removed in all functions. File format is determined automatically now.
• clusterByQuality() clusters now on complexity as well by default.

BUG FIXES

• Corrected bug in order of seqlevels after as(..., 'GRanges').
• Corrected bug in hotspotter() that caused detection of low-abundance hotspots.