Man pages for methylPipe
Base resolution DNA methylation data analysis

BSdata-classClass "BSdata"
BSdataSet-classClass "BSdataSet"
BSpreparePreparing tabular data to be used to feed a BSdata object
chiCombPFisher's method implementation
consolidateDMRsConsolidating Differentially Methylated Regions (DMRs)
extractBinGRangesExtract genomic ranges for a given bin
findDMRIdentifying Differentially Methylated Regions (DMRs)
findPMDsIdentifying Partially Methylated Domains (PMDs)
GEcollection-classClass "GEcollection"
GElist-classClass "GElist"
getCposGet genomic Cxx positons for a series of genomic regions
getCposDensityDetermines the density of genomic Cxx positions for a series...
mapBSdata2GRangesRetrieve mC calls for a GRanges set of genomic regions given...
mCsmoothingSmoothing and plotting methylation data
meth.callFunction to read methylation calls
methstatsExploratory statistics of samples in BSdataSet object
methylPipe-packageAnalysis of base-pair resolution DNA methylation data.
plotMethPlot DNA methylation together with other omics, or annotation...
pool.readsFunction to pool reads of replicates
process.hmcProcessing hmC information from the MLML output
profileDNAmetBinProfile DNA methylation data for a set of genomic regions
splitChrsPartitioning genome in chunks, for parallel computation
tabixdata2GRConvert the list returned by the function scanTabix into a...
methylPipe documentation built on Oct. 31, 2019, 2:15 a.m.