Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.
|Date of publication||None|
|Maintainer||Kamal Kishore <email@example.com>|
BSdata-class: Class "BSdata"
BSdataSet-class: Class "BSdataSet"
BSprepare: Preparing tabular data to be used to feed a BSdata object
chiCombP: Fisher's method implementation
consolidateDMRs: Consolidating Differentially Methylated Regions (DMRs)
extractBinGRanges: Extract genomic ranges for a given bin
findDMR: Identifying Differentially Methylated Regions (DMRs)
findPMDs: Identifying Partially Methylated Domains (PMDs)
GEcollection-class: Class "GEcollection"
GElist-class: Class "GElist"
getCpos: Get genomic Cxx positons for a series of genomic regions
getCposDensity: Determines the density of genomic Cxx positions for a series...
mapBSdata2GRanges: Retrieve mC calls for a GRanges set of genomic regions given...
mCsmoothing: Smoothing and plotting methylation data
meth.call: Function to read methylation calls
methstats: Exploratory statistics of samples in BSdataSet object
methylPipe-package: Analysis of base-pair resolution DNA methylation data.
plotMeth: Plot DNA methylation together with other omics, or annotation...
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
splitChrs: Partitioning genome in chunks, for parallel computation
tabixdata2GR: Convert the list returned by the function scanTabix into a...