read_gff {plyranges} | R Documentation

## 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

[Package plyranges version 1.10.0 Index]