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methylPipe (version 1.4.0)

Base resolution DNA methylation data analysis

Description

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.

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Version

1.4.0

License

GPL(>=2)

Maintainer

Kamal Kishore

Last Published

February 15th, 2017

Functions in methylPipe (1.4.0)

findDMR

Identifying Differentially Methylated Regions (DMRs)

getCposDensity

Determines the density of genomic Cxx positions for a series of genomic regions

Analysis of base-pair resolution DNA methylation data.

plotMeth

Plot DNA methylation together with other omics, or annotation data for a genomic region

getCpos

Get genomic Cxx positons for a series of genomic regions

findPMDs

Identifying Partially Methylated Domains (PMDs)

Preparing tabular data to be used to feed a BSdata object

meth.call

Function to read methylation calls

chiCombP

Fisher's method implementation

methstats

Exploratory statistics of samples in BSdataSet object

splitChrs

Partitioning genome in chunks, for parallel computation

tabixdata2GR

Convert the list returned by the function scanTabix into a GRanges

process.hmc

Processing hmC information from the MLML output

profileDNAmetBin

Profile DNA methylation data for a set of genomic regions

consolidateDMRs

Consolidating Differentially Methylated Regions (DMRs)

extractBinGRanges

Extract genomic ranges for a given bin

mCsmoothing

Smoothing and plotting methylation data

mapBSdata2GRanges

Retrieve mC calls for a GRanges set of genomic regions given a BSdata object for a sample