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A gene's exon, intron and UTR structure on real coordinates

Source: R/gene_model.R
dmsa_gene_model.Rd

Returns one row per drawable feature - coding exon slice, 5' UTR, 3' UTR, or an exon whose coding status the annotation did not resolve - for every transcript of a gene, with strand and genomic start/end. This is what dmsa_plot_locus draws the gene from, and it is deliberately a plain data frame so it can be built, inspected, corrected and cached like any other reference layer in this package.

Usage

dmsa_gene_model(
  gene,
  source = c("auto", "ensembl", "gff", "txdb", "ensdb", "table"),
  file = NULL,
  db = NULL,
  orgdb = NULL,
  table = NULL,
  species = "homo_sapiens",
  genome = "hg38",
  cache = NULL,
  host = "https://rest.ensembl.org",
  quiet = FALSE
)

Arguments

gene

Gene symbol, e.g. "NR3C1".

source

One of "auto", "ensembl", "gff", "txdb", "ensdb", "table". "auto" takes a cached copy if there is one, then Ensembl.

file

GTF/GFF3 path when source = "gff".

db

TxDb or EnsDb object when source is "txdb" / "ensdb".

orgdb

OrgDb for symbol lookup with "txdb" (e.g. org.Hs.eg.db).

table

A data frame already in this shape, when source = "table".

species

Ensembl species name. Default "homo_sapiens".

genome

Genome label recorded on every row. Default "hg38" - the assembly the bundled Alpha coordinates use.

cache

Directory for fetched models, or NULL to disable. Default is a dmsa folder under the session temp directory.

host

Ensembl REST host. NULL disables the network entirely and returns an empty model, which is how you guarantee an offline build.

quiet

Suppress progress messages.

Value

A data frame with the columns in .GM_COLS, class dmsa_gene_model. Zero rows if the model could not be obtained - never a fabricated one.

See also

dmsa_gene_model_check, dmsa_plot_locus

Examples

if (FALSE) { # \dontrun{
## Needs network: one lookup plus one region query per gene.
gm <- dmsa_gene_model("NR3C1")
subset(gm, canonical)[, c("feature", "start", "end", "exon_rank")]

## Or from an annotation you already have, with no network at all:
gm <- dmsa_gene_model("NR3C1", source = "gff", file = "Homo_sapiens.gtf.gz")
} # }