read.gff {ape}

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)