compPvals: compute p-values

In dhelekal/mmdiff3: Statistical Testing for ChIP-Seq data sets

Description

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

Usage

compPvals(MD, dist.method = "MMD", diff.method = "MMD.locfit",
  plot.on = FALSE, verbose = 1)

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)

dhelekal/mmdiff3 documentation built on July 25, 2019, 8:18 p.m.