CpGsDemo                Toy data for the package - 1000 CpG regions to
                        be tested in a GRanges object
M3D-package             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.
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.
determineGroupComps     Creates strings of sample pair comparisons
findComps               Finds columns in the M3D test-statistic matrix
medianFreq              Finds the median
median_freq             Finds the median
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
