# Analysis of Copy Number Variation in Single-Cell-Sequencing Data

## Documentation for package ‘AneuFinder’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

AneuFinder-package | Copy-number detection in WGSCS and Strand-Seq data
aneuBiHMM | Bivariate Hidden Markov Model
AneuFinder | Copy-number detection in WGSCS and Strand-Seq data
Aneufinder | Wrapper function for the 'AneuFinder' package
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)
binned.data | Binned read counts
binning | Bin the genome
binReads | Convert aligned reads from various file formats into read counts in equidistant bins
blacklist | Make a blacklist for genomic regions
breakpointColors | 'AneuFinder' color scheme
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
DNAcopy.findCNVs | Find copy number variations (DNAcopy, univariate)
dzinbinom | The Zero-inflated Negative Binomial Distribution
edivisive.findCNVs | Find copy number variations (edivisive, univariate)
estimateComplexity | Estimate library complexity
export | Export genome browser viewable files
exportCNVs | Export genome browser viewable files
exportGRanges | Export genome browser viewable files
exportReadCounts | 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
HMM.findCNVs | Find copy number variations (univariate)
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.aneuBiHMM | Plotting function for 'aneuBiHMM' objects
plot.aneuHMM | Plotting function for 'aneuHMM' objects
plot.character | Plotting function for saved 'AneuFinder' objects
plot.GRanges | Plotting function for binned read counts
plot.GRangesList | Plotting function for binned read counts (list)
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
pzinbinom | The Zero-inflated Negative Binomial Distribution
qc.bhattacharyya | Quality control measures for binned read counts
qc.entropy | Quality control measures for binned read counts
qc.sos | Quality control measures for binned read counts
qc.spikiness | Quality control measures for binned read counts
qualityControl | Quality control measures for binned read counts
qzinbinom | The Zero-inflated Negative Binomial Distribution
readConfig | Read AneuFinder configuration file
refineBreakpoints | Refine breakpoints
rzinbinom | The Zero-inflated Negative Binomial Distribution
simulateReads | Simulate reads from genome
stateColors | 'AneuFinder' color scheme
strandColors | 'AneuFinder' color scheme
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