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


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Documentation for package ‘methimpute’ version 1.26.0

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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