read.gff {ape} | R Documentation

## 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(".", "?"))

### 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).

### 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 files can also be read but the field names conform to GFF3.

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 <- "ftp://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")
    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)

[Package ape version 4.0 Index]