genomes (version 2.16.0)

read.gff: Read a GFF file from NCBI

Description

Read a GFF file from NCBI genomes ftp (version 3)

Usage

read.gff(file,  locus.tags = TRUE, nrows = -1)

Arguments

file

a GFF file

locus.tags

only return genes with locus tags

nrows

number of rows to read

Value

name. If all rows are returned (locus.tags=FALSE), then score, phase and tags are included. The seqid and source are saved in metadata.

Details

GFF files are available from the NCBI genomes ftp directory, ftp://ftp.ncbi.nih.gov/genomes.

References

see http://www.sequenceontology.org/gff3.shtml for details about Generic Feature Format

See Also

read.ncbi.ftp

Examples

 file<-"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Yersinia_pestis_CO92_uid57621/NC_003132.gff"
 x <-read.gff(file)
 x
metadata(x)