\HeaderA{read.resultsGFF}{Read Nimblegen GFF files}{read.resultsGFF}
\keyword{IO}{read.resultsGFF}
\keyword{manip}{read.resultsGFF}
\begin{Description}\relax
A GFF format file is a quite flexible format for storing genomic
data.  Nimblegen uses these format files as one format for making
chip-chip data available.  This function reads these files, one per
experiment and creates a resulting aGFF-class object.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.resultsGFF(fnames, path = ".", samples = NULL, notes = NULL, skip = 0, sep = "\t", quote = "\"", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fnames}] A vector of filenames
\item[\code{path}] The path to the filenames
\item[\code{samples}] A data.frame containing sample information, one row per
sample, in the same order as the files in fnames
\item[\code{notes}] A character vector for notes--not currently stored
\item[\code{skip}] Number of lines to skip if the file contains a header
\item[\code{sep}] The field separator--should be a tab character for gff
files, but can be set if necessary.
\item[\code{quote}] The text quote character--again not used for gff file, typically
\item[\code{...}] ...
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The output is an aGFF object.
\end{Details}
\begin{Value}
A single aGFF object.
\end{Value}
\begin{Author}\relax
Sean Davis <sdavis2@mail.nih.gov>
\end{Author}
\begin{References}\relax
http://www.sanger.ac.uk/Software/formats/GFF/
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{aGFF-class}{aGFF.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
datdir <- system.file('extdata',package='ACME')
fnames <- dir(datdir)
example.agff <- read.resultsGFF(fnames,path=datdir)
\end{ExampleCode}
\end{Examples}

