Read Nimblegen GFF files

Description

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.

Usage

1
read.resultsGFF(fnames, path = ".", samples = NULL, notes = NULL, skip = 0, sep = "\t", quote = "\"", ...)

Arguments

fnames

A vector of filenames

path

The path to the filenames

samples

A data.frame containing sample information, one row per sample, in the same order as the files in fnames

notes

A character vector for notes–not currently stored

skip

Number of lines to skip if the file contains a header

sep

The field separator–should be a tab character for gff files, but can be set if necessary.

quote

The text quote character–again not used for gff file, typically

...

...

Details

The output is an ACMESet object.

Value

A single ACMESet object.

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

References

http://www.sanger.ac.uk/Software/formats/GFF/

See Also

ACMESet

Examples

1
2
3
datdir <- system.file('extdata',package='ACME')
fnames <- dir(datdir)
example.agff <- read.resultsGFF(fnames,path=datdir)