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.