# Identifies differentially methylated regions across testing groups

## Documentation for package ‘M3D’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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