ape: read.gff – R documentation

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ape

read.gff

Read GFF Files

Description

This function reads a file in general feature format version 3 (GFF3) and returns a data frame.

Usage

read.gff(file, na.strings = c(".", "?"), GFF3 = TRUE)

Arguments

`file`	a file name specified by a character string.
`na.strings`	the strings in the GFF file that will be converted as NA's (missing values).
`GFF3`	a logical value specifying whether if the file is formatted according to version 3 of GFF.

Details

The returned data frame has its (column) names correctly set (see References) and the categorical variables (seqid, source, type, strand, and phase) set as factors.

This function should be more efficient than using read.delim.

GFF2 (aka GTF) files can also be read: use GFF3 = FALSE to have the correct field names. Note that GFF2 files and GFF3 files have the same structure, although some fields are slightly different (see reference).

The file can be gz-compressed (see examples), but not zipped.

Value

NULL

Author(s)

Emmanuel Paradis

References

https://en.wikipedia.org/wiki/General_feature_format

Examples

## Not run: 
## requires to be connected on Internet
d <- "https://ftp.ensembl.org/pub/release-86/gff3/homo_sapiens/"
f <- "Homo_sapiens.GRCh38.86.chromosome.MT.gff3.gz"
download.file(paste0(d, f), "mt_gff3.gz")
## If the above command doesn't work, you may copy/paste the full URL in
## a Web browser instead.
gff.mito <- read.gff("mt_gff3.gz")
## the lengths of the sequence features:
gff.mito$end - (gff.mito$start - 1)
table(gff.mito$type)
## where the exons start:
gff.mito$start[gff.mito$type == "exon"]

## End(Not run)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24