Identifies differentially methylated regions across testing groups


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Documentation for package ‘M3D’ version 1.16.0

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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_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