test_enrichment.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/test_enrichment.R
\name{test_enrichment}
\alias{test_enrichment}
\title{Test enrichment}
\source{
\href{https://www.bioconductor.org/packages/devel/bioc/vignettes/regioneR/inst/doc/regioneR.html}{
See section "3.7A note on reproducibility" for info on setting the seed.}
}
\usage{
test_enrichment(
  grlist1,
  grlist2,
  ntimes = 100,
  genome = "hg19",
  alternative = "auto",
  min.parallel = 1000,
  force.parallel = NULL,
  seed = 2022,
  mc.set.seed = FALSE,
  save_path = tempfile(fileext = "_test_enrichment.rds"),
  verbose = TRUE,
  ...
)
}
\arguments{
\item{grlist1}{First list of \link[GenomicRanges]{GRanges} objects.}

\item{grlist2}{Second list of \link[GenomicRanges]{GRanges} objects.}

\item{ntimes}{number of permutations}

\item{genome}{The reference genome to use. A valid genome object. 
Either a GenomicRanges or data.frame containing one region per whole 
chromosome or a character uniquely identifying a genome in 
BSgenome (e.g. "hg19", "mm10" but not "hg"). 
Internally it uses getGenomeAndMask.}

\item{alternative}{the alternative hypothesis must be one of \code{"greater"}, \code{"less"} or \code{"auto"}. If \code{"auto"}, the alternative will be decided depending on the data.}

\item{min.parallel}{if force.parallel is not specified, this will be used to determine the threshold for parallel computation. If \code{length(A) * ntimes > min.parallel}, it will activate the parallel computation. Single threaded otherwise.}

\item{force.parallel}{logical indicating if the computation must be paralelized.}

\item{seed}{Set the seed for reproducibility.}

\item{mc.set.seed}{"In order to create reproducible code with functions that use random 
numbers such as the permutation testing in \pkg{regioneR} , 
it is necessary to use set.seed. 
However, since \pkg{regioneR} uses parallel to perform the test it is
 also necessary to set the \code{mc.set.seed} parameter to FALSE 
 to ensure reproducibility."}

\item{save_path}{Path to save results to as an \emph{RDS} file.
Set to \code{NULL} to skip this step.}

\item{verbose}{Print messages.}

\item{...}{
  Arguments passed on to \code{\link[regioneR:overlapPermTest]{regioneR::overlapPermTest}}
  \describe{
    \item{\code{A}}{a region set in any of the accepted formats by \code{\link[regioneR]{toGRanges}} (\code{\link{GenomicRanges}}, \code{\link{data.frame}}, etc...)}
    \item{\code{B}}{a region set in any of the accepted formats by \code{\link[regioneR]{toGRanges}} (\code{\link{GenomicRanges}}, \code{\link{data.frame}}, etc...)}
  }}
}
\value{
data.frame
}
\description{
Conduct permutation enrichment tests between all combinations of 
two named lists,
each containing one or more \link[GenomicRanges]{GRanges} objects.
Permutation tests are run using \link[regioneR]{overlapPermTest}.
}
\examples{
dat <- echodata::get_Nalls2019_merged() 
grlist1 <- dat[P<5e-8,]
grlist2 <- dat[Support>0,] 
enrich <- test_enrichment(grlist1 = grlist1,
                          grlist2 = grlist2,  
                          ntimes = 25,
                          force.parallel = FALSE) 
}