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\name{read.helicos.tags}
\alias{read.helicos.tags}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Read in helicos tags }
\description{
Read in Helicos tags
}
\usage{
read.helicos.tags(filename, read.tag.names = F,
fix.chromosome.names = F, include.length.info = T)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{filename}{
filename
}
\item{read.tag.names}{
Read in tag names
}
\item{fix.chromosome.names}{
Do we fix chromosome names
}
\item{include.length.info}{
include length information
}
}
\value{
A list like structure
}
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
Fill in later
}
\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, read.tag.names = F, fix.chromosome.names = F,
include.length.info = T)
{
if (read.tag.names) {
rtn <- as.integer(1)
}
else {
rtn <- as.integer(0)
}
tl <- lapply(.Call("read_helicostabf", path.expand(filename),
rtn), function(d) {
xo <- order(abs(d$t))
d$t <- d$t[xo]
d$n <- d$n[xo]
d$l <- d$l[xo]
if (read.tag.names) {
d$s <- d$s[xo]
}
return(d)
})
if (fix.chromosome.names) {
names(tl) <- gsub("\\.fa", "", names(tl))
}
if (read.tag.names) {
return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl,
function(d) d$n), length = lapply(tl, function(d) d$l),
names = lapply(tl, function(d) d$s)))
}
else {
return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl,
function(d) d$n), length = lapply(tl, function(d) d$l)))
}
}
}
}
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