compute p-values

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Description

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

Usage

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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

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## 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)