\name{dmrFdr}
\alias{dmrFdr}
\title{
Calculate FDR q-values for differentially methylated regions (DMRs)
}
\description{
Estimate false discovery rate q-values for a set of differentially methylated regions using a permutation approach.
}
\usage{
dmrFdr(dmr, compare = 1, numPerms = 1000, seed = NULL, verbose = TRUE)
}
\arguments{
  \item{dmr}{
a dmr object as returned by \code{\link{dmrFinder}}
}
  \item{compare}{
The dmr table for which to calculate DMRs. See details.
}
  \item{numPerms}{
Number of permutations
}
  \item{seed}{
Random seed (for reproducibility)
}
  \item{verbose}{
Boolean
}
}
\details{
This function estimates false discovery rate q-values for a dmr object returned by \code{\link{dmrFinder}}. dmrFinder can return a set of DMR tables with one or more pair-wise comparisons between groups. dmrFdr currently only calculated q-values for one of these at a time. The dmr table to use (if the dmr object contains more than one) is specified by the compare option.
}
\value{
a list object in the same format as the input, but with extra p-val and q-val columns for the tabs element.
}
\author{
Martin Aryee <aryee@jhu.edu>
}


\seealso{
\code{\link{dmrFinder}}
}
\examples{
	if (require(charmData) & require(BSgenome.Hsapiens.UCSC.hg18)) {
		phenodataDir <- system.file("extdata", package="charmData")
		pd <- read.delim(file.path(phenodataDir, "phenodata.txt"))
		pd <- subset(pd, tissue \%in\% c("liver", "colon"))
		# Validate format of sample description file		
		res <- validatePd(pd)
		dataDir <- system.file("data", package="charmData")
		setwd(dataDir)
		# Read in raw data
		rawData <- readCharm(files=pd$filename, sampleKey=pd)
		# Find non-CpG control probes
		ctrlIdx <- getControlIndex(rawData, subject=Hsapiens)
		# Estimate methylation
		p <- methp(rawData, controlIndex=ctrlIdx)
		# Find differentially methylated regions
		grp <- pData(rawData)$tissue
		dmr <- dmrFinder(rawData, p=p, groups=grp, 
			compare=c("liver", "colon"), cutoff=0.95)
		head(dmr$tabs[[1]])
		# Estimate false discovery rate for DMRs
		dmr <- dmrFdr(dmr, numPerms=3, seed=123) 
		head(dmr$tabs[[1]])
	}
}