| 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 |