# Base resolution DNA methylation data analysis

## Documentation for package ‘methylPipe’ version 1.16.0

- 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"