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\name{get.smoothed.tag.density}
\alias{get.smoothed.tag.density}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Calculate chromosome-wide profiles of smoothed tag density }
\description{
Given tag positions, the method calculates for each chromosome a tag
density profile, smoothed by the Gaussian kernel. If the optional
control tags are provided, the difference between ChIP and control tag
density is returned.
}
\usage{
get.smoothed.tag.density(signal.tags,
control.tags = NULL,
bandwidth = 150,
bg.weight = NULL,
tag.shift = 146/2,
step = round(bandwidth/3),
background.density.scaling = T,
rngl = NULL,
scale.by.dataset.size = F)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{signal.tags}{ signal chromosome tag coordinate vectors (e.g. output
of \code{\link{select.informative.tags}} }
\item{control.tags}{ optional control (input) tags }
\item{bandwidth}{ standard deviation of the Gaussian kernel }
\item{bg.weight}{ optional weight by which the background density
should be multipled for scaling. If not supplied, the weight is
calculated based on the ratio of the reduced ChIP to input dataset sizes. }
\item{tag.shift}{ Distance by which the positive and negative strand
tags should be shifted towards eachother. This
normally corresponds to the half of the cross-correlation peak
position (e.g. \code{get.binding.characteristics()}$peak$x/2) }
\item{step}{ The distance between the regularly spaced points for
which the values should be calculated. }
\item{background.density.scaling}{ If TRUE, regions of significant tag
enrichment will be masked out when calculating size ratio of the
signal to control datasets (to estimate ratio of the background tag
density). If FALSE, the dataset ratio will be equal to the ratio of
the number of tags in each dataset.}
\item{rngl}{rngl}
\item{scale.by.dataset.size}{scale.by.dataset.size}
}
\value{
A list of elements corresponding to chromosomes, with each element
being an $x/$y data.frame giving the position and associated tag
density. Use \code{\link{writewig}} to output the structure to a WIG
file.
}
\seealso{ \code{\link{writewig}} }
\examples{
\dontrun{
smoothed.density <- get.smoothed.tag.density(chip.data,
control.tags=input.data,
bandwidth=200,
step=100,
tag.shift=round(binding.characteristics$peak$x/2));
writewig(smoothed.density,
"example.density.wig",
"Example smoothed, background-subtracted tag density");
}
}
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