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\name{read.tagalign.tags}
\alias{read.tagalign.tags}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Read in tagalign tags }
\description{
Fill in later
}
\usage{
read.tagalign.tags(filename, fix.chromosome.names = T, fix.quality = T)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{filename}{
Filename of tag file
}
\item{fix.chromosome.names}{
chromosome names
}
\item{fix.quality}{
fix quality
}
}
\details{
...
}
\value{
a list like structure
}
\references{
spp by kharchenko
}
\author{
Peter K.
}
\note{
Needs further editing
}
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
Buh!
}
\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 (filename, fix.chromosome.names = T, fix.quality = T)
{
tl <- lapply(.Call("read_tagalign", path.expand(filename)),
function(d) {
xo <- order(abs(d$t))
d$t <- d$t[xo]
d$n <- d$n[xo]
if (fix.quality) {
if (min(d$n) < 0.5) {
d$n = ceiling(1000/4^d$n)
}
break.vals <- unique(sort(c(0, unique(d$n))))
d$n <- length(break.vals) - 1 - cut(d$n, breaks = break.vals,
labels = F)
}
return(d)
})
if (fix.chromosome.names) {
names(tl) <- gsub("\\.fa", "", names(tl))
}
return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl,
function(d) d$n)))
}
}
}
|
