GVT file
In plyranges: A fluent interface for manipulating GenomicRanges

Description Usage Arguments Value See Also Examples

This is a lightweight wrapper to the import family of functions defined in rtracklayer.

read_gff(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

read_gff1(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

read_gff2(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

read_gff3(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

`file`	A path to a file or a connection.
`col_names`	An optional character vector for parsing specific columns in `file` that are part of the GFF specification. These should name either fixed fields, like source or type, or, for GFF2 and GFF3, any attribute.
`genome_info`	An optional character string or a Ranges object that contains information about the genome build. For example the UCSC identifier "hg19" will add build information to the returned GRanges.
`overlap_ranges`	An optional Ranges object. Only the intervals in the file that overlap the Ranges will be returned.

A GRanges object

a GRanges object

rtracklayer::GFFFile()

test_path <- system.file("tests", package = "rtracklayer")
# gff3
test_gff3 <- file.path(test_path, "genes.gff3")
gr <- read_gff3(test_gff3)
gr
# alternatively with read_gff
gr <- read_gff(test_gff3, genome_info = "hg19")
gr