\name{DMP}
\alias{hello}
\title{Find differentially methylated pathways}
\description{
Determine association between methylation pattern in a pathway (or any other gene-set) and a phenotype.
}
\usage{
DMP <- function(dat, pheno, covar=NA, pathout=".", genesetpath=".", minNgenes = 10, maxNgenes = 300,
                annotation=".", P.thresh=0.05, maxN=5, NPERM=100, P_THRESH=0.01, R_THRESH = 0.2, distCPG = 500,
                skipPermuting=TRUE, verbose=TRUE )
}
\arguments{
  \item(dat){A Beta value methylation matrix.}
  \item(pheno){Phenotype to be testded matrix.}
  \item(pathout){Path to output file.}
  \item(genesetpath){Path to file with gene set descriptions.}
  \item(minNgenes){Minimum number of genes a pathway can have.}
  \item(maxNgenes){Maximum number of genes a pathway can have.}
  \item(annotation){data.frame with CpG annotation.}
  \item(P.thresh){Significance threshold for CpGs within pathway.}
  \item(maxN){Maximum number of significant CpGs to include.}
  \item(NPERM){Number of permutations.}
  \item(P_THRESH){Significance threshold of original P-value to start permutations.}
  \item(R_THRESH){Correlation threshold to discard neighboring correlated CpGs.}
  \item(distCPG){Distance (pb) at which neighboring CpGs are examined.}
  \item(skipPermuting){Skip permutation if original pathwa P-value does not fulfill threshold.}
  \item(verbose){A boolean to print out messages}

}
\examples{
hello()
}
