Base resolution DNA methylation data analysis

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Documentation for package ‘methylPipe’ version 1.41.0

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

Help Pages

methylPipe-package	Analysis of base-pair resolution DNA methylation data.
$,BSdataSet	Class "BSdataSet"
$,GElist	Class "GElist"
$-method	Class "BSdataSet"
$-method	Class "GElist"
binC	Class "GEcollection"
binC-method	Class "GEcollection"
binmC	Class "GEcollection"
binmC-method	Class "GEcollection"
binrC	Class "GEcollection"
binrC-method	Class "GEcollection"
binscore	Class "GEcollection"
binscore-method	Class "GEcollection"
binscore<-	Class "GEcollection"
binscore<--method	Class "GEcollection"
BSdata	Class "BSdata"
BSdata-class	Class "BSdata"
BSdataSet	Class "BSdataSet"
BSdataSet-class	Class "BSdataSet"
BSprepare	Preparing tabular data to be used to feed a BSdata object
chiCombP	Fisher's method implementation
chr	Class "GEcollection"
chr-method	Class "GEcollection"
consolidateDMRs	Consolidating Differentially Methylated Regions (DMRs)
extractBinGRanges	Extract genomic ranges for a given bin
findDMR	Identifying Differentially Methylated Regions (DMRs)
findDMR,methylPipe,BSdataSet	Identifying Differentially Methylated Regions (DMRs)
findDMR-method	Identifying Differentially Methylated Regions (DMRs)
findDMR-methods	Identifying Differentially Methylated Regions (DMRs)
findPMDs	Identifying Partially Methylated Domains (PMDs)
findPMDs,methylPipe,BSdata	Identifying Partially Methylated Domains (PMDs)
findPMDs-method	Identifying Partially Methylated Domains (PMDs)
findPMDs-methods	Identifying Partially Methylated Domains (PMDs)
GEcollection	Class "GEcollection"
GEcollection-class	Class "GEcollection"
GElist	Class "GElist"
GElist-class	Class "GElist"
getCpos	Get genomic Cxx positons for a series of genomic regions
getCposChr	Get genomic Cxx positons for a series of genomic regions
getCposDensity	Determines the density of genomic Cxx positions for a series of genomic regions
length	Class "GEcollection"
length-method	Class "BSdataSet"
length-method	Class "GEcollection"
length-method	Class "GElist"
mapBSdata2GRanges	Retrieve mC calls for a GRanges set of genomic regions given a BSdata object for a sample
mapBSdata2GRangesBin	Retrieve mC calls for a GRanges set of genomic regions given a BSdata object for a sample
mCsmoothing	Smoothing and plotting methylation data
mCsmoothing,methylPipe,BSdata	Smoothing and plotting methylation data
mCsmoothing-method	Smoothing and plotting methylation data
mCsmoothing-methods	Smoothing and plotting methylation data
meth.call	Function to read methylation calls
methstats	Exploratory statistics of samples in BSdataSet object
methstats,methylPipe,BSdataSet	Exploratory statistics of samples in BSdataSet object
methstats-method	Exploratory statistics of samples in BSdataSet object
methstats-methods	Exploratory statistics of samples in BSdataSet object
methylPipe	Analysis of base-pair resolution DNA methylation data.
nbins	Class "GEcollection"
nbins-method	Class "GEcollection"
plotMeth	Plot DNA methylation together with other omics, or annotation data for a genomic region
pool.reads	Function to pool reads of replicates
process.hmc	Processing hmC information from the MLML output
profileDNAmetBin	Profile DNA methylation data for a set of genomic regions
profileDNAmetBinParallel	Profile DNA methylation data for a set of genomic regions
show-method	Class "BSdata"
show-method	Class "BSdataSet"
show-method	Class "GEcollection"
show-method	Class "GElist"
splitChrs	Partitioning genome in chunks, for parallel computation
tabixdata2GR	Convert the list returned by the function scanTabix into a GRanges
[-method	Class "BSdataSet"
[-method	Class "GElist"
[[-method	Class "BSdataSet"
[[-method	Class "GElist"
[[<--method	Class "BSdataSet"
[[<--method	Class "GElist"