Built-in protein-coding gene annotations — gene

Return a data.frame of protein-coding gene positions bundled with ggwas, ready for gene_track(), locus_plot() or manhattan_genes(), so that regional and gene-labelled plots work without downloading a GTF. Data are derived from Ensembl (GRCh38 release 103; GRCh37 release 75) and restricted to protein-coding genes.

Usage

gene_annotation(build = c("GRCh38", "GRCh37"))

Arguments

build: Genome build: "GRCh38" (default) or "GRCh37".

Value

A data.frame with columns chr (integer), start, end, gene, and strand.

Examples

genes <- gene_annotation("GRCh38")
head(genes)
#>   chr  start    end   gene strand
#> 1   1  65419  71585  OR4F5      +
#> 2   1 450740 451678 OR4F29      -
#> 3   1 685679 686673 OR4F16      -
#> 4   1 923923 944575 SAMD11      +
#> 5   1 944203 959309  NOC2L      -
#> 6   1 960584 965719 KLHL17      +

# Gene track for a region, no GTF needed
gene_track(genes, region_chr = 6, region_start = 25e6, region_end = 34e6)