compPvals: compute p-values
In MMDiff2: Statistical Testing for ChIP-Seq data sets

Description Usage Arguments Value See Also Examples

This function determines peak-specific p-values based on distances between sample histograms.

1	compPvals(MD, dist.method = "MMD", diff.method = "MMD.locfit")

`MD`	DBAmmd Object. This Object can be created using `DBAmmd()`.
`dist.method`	specify method used for distances between samples. Currently only Maximum Mean Discrepancy (MMD) and Kolmogorov-Smirnov (KS) implemented. (DEFAULT: 'MMD')
`diff.method`	method used to determine p-values and false discovery rates. Currently only 'MMD.locfit' implemented. (DEFAULT: 'MMD.locfit')

DBAmmd object with updated Contrasts slot.

DBAmmd,reportResults, plotDists,compDists

## Example using a small data set provided with this package:

data("MMD")
MMD.1 <- setContrast(MMD,contrast='byCondition')
MMD.1 <- compPvals(MMD.1)
reportResults(MMD.1)