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_Para |
Computes the components of the M3D test-statistic over all regions for all sample-pairs. |
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. |
medianFreq |
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. |
plotMethProfile |
Plots methylation profiles over a specific region |
pvals |
Computes p-values |
readENCODEdata |
Reads in ENCODE RRBS data |
rrbsDemo |
Toy data for the package - methylation data for cytosines sites within the testing regions only, in an rrbs object. |