Parse a GTF or GFF3 annotation file and return a data.frame of gene
positions ready for use with gene_track() or locus_plot().
Supports .gz compressed files.
Usage
read_gtf(
path,
feature_type = "gene",
gene_name_attr = c("gene_name", "Name", "gene"),
gene_id_attr = "gene_id",
biotype = NULL
)Arguments
- path
Path to GTF or GFF3 file (plain text or gzipped).
- feature_type
Feature type to extract (column 3 of GTF). Default
"gene".- gene_name_attr
Attribute key(s) to use as gene name, tried in order. For GTF:
"gene_name", for GFF3:"Name".- gene_id_attr
Attribute key for gene ID (e.g. ENSG...).
- biotype
Character vector of gene biotypes to keep, e.g.
"protein_coding". If NULL (default), all biotypes are returned.
Value
A data.frame with columns: chr (integer), start, end, gene,
strand, gene_id. Ready for gene_track() or
locus_plot(gene_data = ...).
Examples
f <- system.file("extdata", "example.gtf", package = "ggwas")
genes <- read_gtf(f)
#> Read 4 gene features from example.gtf.
head(genes)
#> chr start end strand gene gene_id
#> 1 1 1000000 2000000 + GeneA ENSG00000001
#> 2 1 5000000 6500000 - GeneB ENSG00000002
#> 3 1 8000000 9000000 + GeneC ENSG00000003
#> 4 2 3000000 4000000 + GeneD ENSG00000004