Conveniently look up the region of a gene by gene symbol. The value returned by this function
can be used as the region
argument for trackplot functions such as
trackplot_coverage()
or trackplot_gene()
Usage
gene_region(
genes,
gene_symbol,
extend_bp = c(10000, 10000),
gene_mapping = human_gene_mapping
)
Arguments
- genes
Transcipt features given as GRanges, data.frame, or list. See
help("genomic-ranges-like")
for details on format and coordinate systems. Required attributes:chr
,start
,end
: genomic positionstrand
: +/- or TRUE/FALSE for positive or negative strandgene_name
: Symbol or gene ID
- gene_symbol
Name of gene symbol or ID
- extend_bp
Bases to extend region upstream and downstream of gene. If length 1, extension is symmetric. If length 2, provide upstream extension then downstream extension as positive distances.
- gene_mapping
Named vector where names are gene symbols or IDs and values are canonical gene symbols
Examples
## Prep data
genes <- read_gencode_transcripts(
file.path(tempdir(), "references"), release = "42",
annotation_set = "basic",
features = "transcript"
)
## Get gene region
gene_region(genes, "CD19", extend_bp = 1e5)
#> $chr
#> [1] "chr16"
#>
#> $start
#> [1] 28831970
#>
#> $end
#> [1] 29039342
#>