methylPipe (version 1.6.2)

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

1.6.2

License

GPL(>=2)

Maintainer

Kamal Kishore

Last Published

February 15th, 2017

Functions in methylPipe (1.6.2)

extractBinGRanges

Extract genomic ranges for a given bin

Exploratory statistics of samples in BSdataSet object

splitChrs

Partitioning genome in chunks, for parallel computation

methylPipe-package

Analysis of base-pair resolution DNA methylation data.

tabixdata2GR

Convert the list returned by the function scanTabix into a GRanges

findPMDs

Identifying Partially Methylated Domains (PMDs)

getCpos

Get genomic Cxx positons for a series of genomic regions

findDMR

Identifying Differentially Methylated Regions (DMRs)

profileDNAmetBin

Profile DNA methylation data for a set of genomic regions

chiCombP

Fisher's method implementation

pool.reads

Function to pool reads of replicates

mapBSdata2GRanges

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

getCposDensity

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

consolidateDMRs

Consolidating Differentially Methylated Regions (DMRs)

mCsmoothing

Smoothing and plotting methylation data

process.hmc

Processing hmC information from the MLML output

BSprepare

Preparing tabular data to be used to feed a BSdata object

plotMeth

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

meth.call

Function to read methylation calls

GEcollection-class

Class "GEcollection"