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 |