compPvals {MMDiff2} | R Documentation

## compute p-values

### Description

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

### Usage

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

### Arguments

`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')

### Value

DBAmmd object with updated `Contrasts` slot.

### See Also

`DBAmmd`,`reportResults`, `plotDists`,`compDists`

### Examples

    ## 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)

[Package MMDiff2 version 1.8.0 Index]