Identifies differentially methylated regions across testing groups.


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Documentation for package ‘M3D’ version 1.1.4

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M3D-package Non-parametric statistical testing
CpGsDemo Toy data for the package - 1000 CpG regions to be tested in a GRanges object
determineGroupComps Creates strings of sample pair comparisons
findComps Finds columns in the M3D test-statistic matrix
M3D Non-parametric statistical testing
M3D_Para Computes the components of the M3D test-statistic over all regions for all sample-pairs.
M3D_Single Computes the components of the M3D test-statistic over one region for 2 samples
M3D_Wrapper Computes the components of the M3D test-statistic over all regions for all sample-pairs.
medianFreq Finds the median
MMDlistDemo Toy data for the package - the output of the M3D_Wrapper function.
PDemo Toy data for the package - the output of the pvals function.
plotMethProfile Plots methylation profiles over a specific region
pvals Computes p-values
readENCODEdata Reads in ENCODE RRBS data
rrbsDemo Toy data for the package - methylation data for cytosines sites within the testing regions only, in an rrbs object.