diff spp/man/get.mser.Rd @ 6:ce08b0efa3fd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/man/get.mser.Rd	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,46 @@
+\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}}}
+}
+\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.
+}