# Imputation-guided re-construction of complete methylomes from WGBS data

## Documentation for package ‘methimpute’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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