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

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Documentation for package ‘AneuFinder’ version 1.32.0

• 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