Imputation-guided re-construction of complete methylomes from
WGBS data
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Documentation for package ‘methimpute’ version 1.20.0
Help Pages
| methimpute-package | methIMPUTE: Imputation-guided methylation status calling for WGBS-seq |
| arabidopsis_chromosomes | Chromosome lengths for Arabidopsis |
| arabidopsis_genes | Gene coordinates for Arabidopsis (chr1) |
| arabidopsis_TEs | Transposable element coordinates for Arabidopsis (chr1) |
| arabidopsis_toydata | Toy data for Arabidopsis (200.000bp of chr1) |
| binCounts | Methimpute binning functions |
| binMethylome | Methimpute binning functions |
| binning | Methimpute binning functions |
| binomialTestMethylation | Call methylation status |
| binPositions | Methimpute binning functions |
| callMethylation | Call methylation status |
| callMethylationSeparate | Call methylation status |
| collapseBins | Collapse consecutive bins |
| distanceCorrelation | Distance correlation |
| estimateTransDist | 'transDist' parameter |
| exportMethylome | Export a methylome |
| extractCytosinesFromFASTA | Extract cytosine coordinates |
| getDistinctColors | Get distinct colors |
| getPosteriors | Get original posteriors |
| getStateColors | Get state colors |
| import | Methimpute data import |
| importBismark | Methimpute data import |
| importBSMAP | Methimpute data import |
| importBSSeeker | Methimpute data import |
| importMethylpy | Methimpute data import |
| importRene | Import a Rene methylation extractor file |
| inflateMethylome | Inflate an imported methylation extractor file |
| loadFromFiles | Load 'methimpute' objects from file |
| methimpute | methIMPUTE: Imputation-guided methylation status calling for WGBS-seq |
| methimpute-objects | methimpute objects |
| methimputeBinomialHMM | methimputeBinomialHMM |
| methimputeData | methimputeData |
| parameterScan | Perform a parameter scan |
| plotConvergence | Methimpute plotting functions |
| plotEnrichment | Methimpute plotting functions |
| plotHistogram | Methimpute plotting functions |
| plotPosteriorDistance | Methimpute plotting functions |
| plotScatter | Methimpute plotting functions |
| plotting | Methimpute plotting functions |
| plotTransitionProbs | Methimpute plotting functions |
| print.methimputeBinomialHMM | Print model object |
| transCoord | Transform genomic coordinates |