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\name{get.mser}
\alias{get.mser}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Calculate minimal saturated enrichment fold ratio }
\description{
Determine if the dataset has reached absolute saturation, or otherwise
find minimal fold enrichment ratio above which the detection of peaks
has stabilized enough to meet the saturation criteria.
}
\usage{
get.mser(signal.data,
control.data,
n.chains = 5,
step.size = 1e+05,
chains = NULL,
cluster = NULL,
test.agreement = 0.99,
return.chains = F,
enrichment.background.scales = c(1),
n.steps = 1, ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{signal.data}{ signal tag vector list }
\item{control.data}{ control tag vector list }
\item{n.chains}{ number of dataset subsamples to use }
\item{step.size}{ subsampling step describing the saturation
criteria. The criteria requires the set of detected binding sites to
be stable (as described by the \code{test.agreement} param) when the
number of tags in the dataset is reduced by \code{step.size}. The
value can either be an integer above one, in which case it specifies a fixed
number of tags, or a real value below one, in which case it
specifies the fraction of tags that should be removed (e.g. 0.1 will
remove 10% of tags).
}
\item{test.agreement}{ Fraction of the detected peaks that should
agree between the full and subsampled datasets. }
\item{chains}{ optional parameter, giving pre-calculated chains }
\item{cluster}{ optional \code{snow} cluster to parallelize processing }
\item{return.chains}{ whether subsampled dataset results should be returned as
well }
\item{enrichment.background.scales}{ one or multiple window scales at
which the background tag density should be assessed. See
\code{enrichment.background.scales} in
\code{\link{find.binding.positions}}. If multiple scales are provided,
multiple MSER estimates will be returned.}
\item{\dots}{ additional parameters should be the same as those passed
to the \code{\link{find.binding.positions}}}
\item{n.steps}{n.steps}
}
\value{
A single, or multple (if multiple \code{enrichment.background.scales} were
provided) MSER value. A value of 1 or very close to it implies that
the dataset has reached absolute saturation based on the given criteria.
}
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