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\name{get.smoothed.enrichment.mle2}
\alias{get.smoothed.enrichment.mle2}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Calculate background input controlled chromosome-wide
profiles of smoothed enrichment estimate }
\description{
Given signal and control tag positions, the method calculates log2
signal to control enrichment esimates (maximum likelihood) for each
chromosome, based on the smoothed tag density profile
(see \link{get.smoothed.tag.density}).
}
\usage{
get.smoothed.enrichment.mle2(signal.tags1, control.tags1,
signal.tags2, control.tags2,
tag.shift = 146/2, background.density.scaling = F,
pseudocount = 1, bg.weight1 = NULL,
bg.weight2 = NULL,
rngl = NULL, chrl = NULL, ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{signal.tags1}{
Parameter
}
\item{control.tags1}{
Parameter
}
\item{signal.tags2}{
Parameter
}
\item{control.tags2}{
Parameter
}
\item{tag.shift}{
Parameter
}
\item{background.density.scaling}{
Parameter
}
\item{pseudocount}{
Parameter
}
\item{bg.weight1}{
Parameter
}
\item{bg.weight2}{
Parameter
}
\item{rngl}{
Parameter
}
\item{chrl}{
Parameter
}
\item{\dots}{
Parameter
}
}
\value{
A list of elements corresponding to chromosomes, with each element
being an $x/$y data.frame giving the position and associated
log2 signal/control enrichment estimate.
}
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
\code{\link{get.smoothed.enrichment.mle}}
}
\examples{
\dontrun{
##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (signal.tags1, control.tags1, signal.tags2, control.tags2,
tag.shift = 146/2, background.density.scaling = F, pseudocount = 1,
bg.weight1 = NULL, bg.weight2 = NULL, rngl = NULL, chrl = NULL,
...)
{
if (is.null(chrl)) {
chrl <- intersect(names(signal.tags1), names(signal.tags2))
names(chrl) <- chrl
}
if (is.null(rngl)) {
rngl <- lapply(chrl, function(chr) range(c(range(abs(signal.tags1[[chr]] +
tag.shift)), range(abs(signal.tags2[[chr]] + tag.shift)))))
}
else {
chrl <- names(rngl)
names(chrl) <- chrl
}
ssd1 <- get.smoothed.tag.density(signal.tags1, rngl = rngl,
..., scale.by.dataset.size = F)
ssd2 <- get.smoothed.tag.density(signal.tags2, rngl = rngl,
..., scale.by.dataset.size = F)
csd1 <- get.smoothed.tag.density(control.tags1, rngl = rngl,
..., scale.by.dataset.size = F)
csd2 <- get.smoothed.tag.density(control.tags2, rngl = rngl,
..., scale.by.dataset.size = F)
if (is.null(bg.weight1)) {
bg.weight1 <- dataset.density.ratio(signal.tags1, control.tags1,
background.density.scaling = background.density.scaling)
}
if (is.null(bg.weight2)) {
bg.weight2 <- dataset.density.ratio(signal.tags2, control.tags2,
background.density.scaling = background.density.scaling)
}
cmle <- lapply(chrl, function(chr) {
d <- ssd1[[chr]]
d$y <- log2(ssd1[[chr]]$y + pseudocount * bg.weight1) -
log2(csd1[[chr]]$y + pseudocount) - log2(bg.weight1) -
log2(ssd2[[chr]]$y + pseudocount * bg.weight2) +
log2(csd2[[chr]]$y + pseudocount) + log2(bg.weight2)
return(d)
})
}
}
}
|
