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M3D (version 1.6.2)

Identifies differentially methylated regions across testing groups

Description

This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.

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Version

Version

1.6.2

License

Artistic License 2.0

Maintainer

Tom Mayo

Last Published

February 15th, 2017

Functions in M3D (1.6.2)

MMDlistDemo

Toy data for the package - the output of the M3D_Wrapper function.
readENCODEdata

Reads in ENCODE RRBS data
M3D_Single

Computes the components of the M3D test-statistic over one region for 2 samples
PDemo

Toy data for the package - the output of the pvals function.
findComps

Finds columns in the M3D test-statistic matrix
CpGsDemo

Toy data for the package - 1000 CpG regions to be tested in a GRanges object
plotMethProfile

Plots methylation profiles over a specific region
determineGroupComps

Creates strings of sample pair comparisons
M3D_Para

Computes the components of the M3D test-statistic over all regions for all sample-pairs.
medianFreq

Finds the median
pvals

Computes p-values
rrbsDemo

Toy data for the package - methylation data for cytosines sites within the testing regions only, in an rrbs object.
M3D_Wrapper

Computes the components of the M3D test-statistic over all regions for all sample-pairs.
M3D-package

Non-parametric statistical testing