Identifies differentially methylated regions across testing groups

Documentation for package ‘M3D’ version 1.12.0

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_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.
M3D_Wrapper_lite	Computes the components of the M3D test-statistic over all regions for all sample-pairs.
medianFreq	Finds the median
median_freq	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.
plotCoverageSampleProfiles	Plots coverage profiles over a specific region
plotMethProfile	Plots methylation profiles over a specific region
plotMethSampleProfiles	Plots methylation profiles over a specific region
pvals	Computes p-values
pvals_lite	Computes p-values
readBedFiles	Reads in bed file to make RRBS data
readBedRaw	Reads in RRBS data in raw format to be processed later
rrbsDemo	Toy data for the package - methylation data for cytosines sites within the testing regions only, in an rrbs object.
test_colData_structure	Tests that the files are specified in a workable order for M3D to run