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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/man/get.mser.interpolation.Rd	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,56 @@
+\name{get.mser.interpolation}
+\alias{get.mser.interpolation}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Interpolate MSER dependency on the tag count }
+\description{
+  MSER generally decreases with increasing sequencing depth. This
+  function interpolates the dependency of MSER on tag counts as a
+  log-log linear function. The log-log fit is used to estimate the depth
+  of sequencing required to reach desired \code{target.fold.enrichment}.
+}
+\usage{
+get.mser.interpolation(signal.data, control.data, target.fold.enrichment = 5, n.chains = 10, n.steps = 6, step.size = 1e+05, chains = NULL, test.agreement = 0.99, return.chains = F, enrichment.background.scales = c(1), excluded.steps = c(seq(2, n.steps - 2)), ...)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{signal.data}{ signal chromosome tag vector list }
+  \item{control.data}{ control chromosome tag vector list }
+  \item{target.fold.enrichment}{ target MSER for which the depth should
+    be estimated}
+  \item{n.steps}{ number of steps in each subset chain. }
+  \item{step.size}{ Either number of tags or fraction of the dataset
+    size, see \code{step.size} parameter for \code{\link{get.mser}}. }
+  \item{test.agreement}{ Fraction of the detected peaks that should
+    agree between the full and subsampled datasets. See \code{test.agreement} parameter for \code{\link{get.mser}}}
+  \item{n.chains}{ number of random subset chains }
+  \item{chains}{ optional structure of pre-calculated chains
+    (e.g. generated by an earlier call with \code{return.chains=T}.}
+  
+  \item{return.chains}{ whether to return peak predictions calculated on
+  random chains. These can be passed back using \code{chains} argument
+  to skip subsampling/prediction steps, and just recalculate the depth
+  estimate for a different MSER.}
+  \item{enrichment.background.scales}{ see \code{enrichment.background.scales} parameter for \code{\link{get.mser}} }
+  \item{excluded.steps}{ Intermediate subsampling steps that should be excluded from
+  the chains to speed up the calculation. By default, all intermediate
+  steps except for first two and last two are skipped. Adding
+  intermediate steps improves interpolation at the expense of
+  computational time.}
+  \item{\dots}{ additional parameters are passed to \code{\link{get.mser}} }
+}
+\details{
+  To simulate sequencing growth, the method calculates peak predictions
+  on random chains. Each chain is produced by sequential random
+  subsampling of the original data. The number of steps in the chain
+  indicates how many times the random subsampling will be performed.
+}
+\value{
+  Normally reurns a list, specifying for each backgroundscale:
+  \item{prediction}{estimated sequencing depth required to reach
+  specified target MSER}
+  \item{log10.fit}{linear fit model, a result of \code{lm()} call}
+
+  If \code{return.chains=T}, the above structure is returned under
+  \code{interpolation} field, along with \code{chains} field containing
+  results of \code{\link{find.binding.positions}} calls on subsampled chains.
+}