read.resultsGFF: Read Nimblegen GFF files

In ACME: Algorithms for Calculating Microarray Enrichment (ACME)

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 ACMESet object.

Value

A single ACMESet object.

Author(s)

Sean Davis <[e-mail]>

References

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

See Also

ACMESet

Examples

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

ACME documentation built on Nov. 8, 2020, 7:51 p.m.