read.resultsGFF {ACME} | R Documentation

## 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

    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 aGFF object.

### Value

A single aGFF object.

### Author(s)

Sean Davis <sdavis2@mail.nih.gov>

### References

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

### See Also

`aGFF-class`

### Examples

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

[Package ACME version 1.10.0 Index]