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


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Documentation for package ‘AneuFinder’ version 1.32.0

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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