reportResults: report results

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

Description

retrieve results of differential binding analysis

Usage

reportResults(MD, diff.method = "MMD.locfit", th = 0.1, Peak.id = NULL,
  whichContrast = 1, rm.oulier = TRUE, bUsePval = FALSE)

Arguments

MD	DBAmmd Object. This Object can be created using DBAmmd().
diff.method	method used to determine p-values and false discovery rates. Currently only 'MMD.locfit' implemented. (DEFAULT: 'MMD.locfit')
th	significance threshold for differential called peaks (DEFAULT: 0.1)
Peak.id	Peak id to specify which Peak to plot. (coresponding to names of Regions(MD))
whichContrast	index determining which of the set contrast should be used. (DEFAULT: 1)
rm.oulier	if TRUE, significant peaks with high within-group distances are not reported. (DEFAULT: TRUE)
bUsePval	if TRUE p-values instead of FDRs are used (DEFAULT: FALSE)

Examples

data("MMD")
res <- reportResults(MMD)

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