AneuFinder-package      Copy-number detection in WGSCS and Strand-Seq
                        data
Aneufinder              Wrapper function for the 'AneuFinder' package
DNAcopy.findCNVs        Find copy number variations (DNAcopy,
                        univariate)
HMM.findCNVs            Find copy number variations (univariate)
aneuBiHMM               Bivariate Hidden Markov Model
aneuHMM                 Hidden Markov Model
annotateBreakpoints     Annotate breakpoints
bam2GRanges             Import BAM file into GRanges
bed2GRanges             Import BED file into GRanges
bi.edivisive.findCNVs   Find copy number variations (edivisive,
                        bivariate)
biDNAcopy.findCNVs      Find copy number variations (DNAcopy,
                        bivariate)
biHMM.findCNVs          Find copy number variations (bivariate)
binReads                Convert aligned reads from various file formats
                        into read counts in equidistant bins
binned.data             Binned read counts
binning                 Bin the genome
blacklist               Make a blacklist for genomic regions
clusterByQuality        Cluster based on quality variables
clusterHMMs             Cluster objects
collapseBins            Collapse consecutive bins
colors                  'AneuFinder' color scheme
compareMethods          Compare copy number calling methods
compareModels           Compare copy number models
consensusSegments       Make consensus segments
correctGC               GC correction
edivisive.findCNVs      Find copy number variations (edivisive,
                        univariate)
estimateComplexity      Estimate library complexity
export                  Export genome browser viewable files
filterSegments          Filter segments by minimal size
findCNVs                Find copy number variations
findCNVs.strandseq      Find copy number variations (strandseq)
findHotspots            Find breakpoint hotspots
fixedWidthBins          Make fixed-width bins
getBreakpoints          Extract breakpoints
getDistinctColors       Get distinct colors
getQC                   Obtain a data.frame with quality metrics
getSCEcoordinates       Get SCE coordinates
heatmapAneuploidies     Plot aneuploidy state
heatmapGenomewide       Genome wide heatmap of CNV-state
heatmapGenomewideClusters
                        Plot heatmaps for quality control
hotspotter              Find hotspots of genomic events
hotspotter.variable     Find hotspots of genomic events
importBed               Read bed-file into GRanges
initializeStates        Initialize state factor levels and
                        distributions
karyotypeMeasures       Measures for Karyotype Heterogeneity
loadFromFiles           Load 'AneuFinder' objects from file
mergeStrandseqFiles     Merge Strand-seq libraries
plot.GRanges            Plotting function for binned read counts
plot.GRangesList        Plotting function for binned read counts (list)
plot.aneuBiHMM          Plotting function for 'aneuBiHMM' objects
plot.aneuHMM            Plotting function for 'aneuHMM' objects
plot.character          Plotting function for saved 'AneuFinder'
                        objects
plotHeterogeneity       Heterogeneity vs. Aneuploidy
plotHistogram           Plot a histogram of binned read counts with
                        fitted mixture distribution
plotKaryogram           Karyogram-like chromosome overview
plotProfile             Read count and CNV profile
plot_pca                Perform a PCA for copy number profiles
print.aneuBiHMM         Print aneuBiHMM object
print.aneuHMM           Print aneuHMM object
qualityControl          Quality control measures for binned read counts
readConfig              Read AneuFinder configuration file
refineBreakpoints       Refine breakpoints
simulateReads           Simulate reads from genome
subsetByCNVprofile      Get IDs of a subset of models
transCoord              Transform genomic coordinates
variableWidthBins       Make variable-width bins
writeConfig             Write AneuFinder configuration file
zinbinom                The Zero-inflated Negative Binomial
                        Distribution
