Man pages for AneuFinder
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
| aneuBiHMM | Bivariate Hidden Markov Model |
| Aneufinder | Wrapper function for the 'AneuFinder' package |
| AneuFinder-package | Copy-number detection in WGSCS and Strand-Seq data |
| aneuHMM | Hidden Markov Model |
| annotateBreakpoints | Annotate breakpoints |
| bam2GRanges | Import BAM file into GRanges |
| bed2GRanges | Import BED file into GRanges |
| biDNAcopy.findCNVs | Find copy number variations (DNAcopy, bivariate) |
| bi.edivisive.findCNVs | Find copy number variations (edivisive, 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... |
| 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 |
| DNAcopy.findCNVs | Find copy number variations (DNAcopy, univariate) |
| 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 |
| 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... |
| plotKaryogram | Karyogram-like chromosome overview |
| plot_pca | Perform a PCA for copy number profiles |
| plotProfile | Read count and CNV profile |
| 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 |
