io-gff-read: Read a GFF/GTF/GVT file

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

Read a GFF/GTF/GVT file

Description

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

Usage

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)

Arguments

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.

Value

A GRanges object

a GRanges object

See Also

rtracklayer::GFFFile()

Examples

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

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.