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


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Documentation for package ‘AneuFinder’ version 1.0.3

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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
bam2GRanges Import BAM file into GRanges
bed2GRanges Import BED file into GRanges
binned.data Binned read counts
binning Bin the genome
binReads Convert aligned reads from various file formats into read counts in equidistant bins
bivariate.findCNVs Find copy number variations (bivariate)
blacklist Make a blacklist for genomic regions
clusterByQuality Cluster based on quality variables
collapseBins Collapse consecutive bins
colors 'AneuFinder' color scheme
correctGC GC correction
correctMappability Mappability correction
deltaWCalculator Calculate deltaWs
dzinbinom The Zero-inflated Negative Binomial Distribution
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
findSCEs Find sister chromatid exchanges
fixedWidthBins Make fixed-width bins
getSCEcoordinates Get SCE coordinates
getSegments Extract segments and cluster
heatmapAneuploidies Plot aneuploidy state
heatmapGenomewide Genome wide heatmap of CNV-state
hotspotter Find hotspots of genomic events
importBed Read bed-file into GRanges
initializeStates Initialize state factor levels and distributions
karyotypeMeasures Measures for Karyotype Heterogeneity
loadGRangesFromFiles Load GRanges from files
loadHmmsFromFiles Load HMMs from files
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
plotBinnedDataHistogram Plot a histogram of binned read counts
plotKaryogram Karyogram-like chromosome overview
plotProfile Read count and CNV profile
plotUnivariateHistogram Plot a histogram of binned read counts with fitted mixture distribution
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.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
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
univariate.findCNVs Find copy number variations (univariate)
variableWidthBins Make variable-width bins
writeConfig Write AneuFinder configuration file
zinbinom The Zero-inflated Negative Binomial Distribution