get_variant_consequences: Retrieve variant consequences

In ramiromagno/ensemblr: R Client for the Ensembl REST API

Retrieve variant consequences

Description

This function retrieves variant consequence types. For more details check Ensembl Variation - Calculated variant consequences.

Usage

get_variant_consequences(verbose = FALSE, warnings = TRUE)

Arguments

verbose	Whether to be chatty about the underlying requests.
warnings	Whether to print warnings.

Details

A rule-based approach is used to predict the effects that each allele of a variant may have on each transcript. These effects are variant consequences, that are catalogued as consequence terms, defined by the Sequence Ontology.

See below a diagram showing the location of each display term relative to the transcript structure:

Value

A tibble, each row being a variant consequence, of four variables:

SO_accession

Sequence Ontology accession, e.g., 'SO:0001626'.

SO_term

Sequence Ontology term, e.g., 'incomplete_terminal_codon_variant'.

label

Display term.

description

Sequence Ontology description.

Ensembl REST API endpoints

get_variant_consequence_types makes GET requests to /info/variation/consequence_types.

Examples

# Retrieve variant consequence types
get_variant_consequences()

ramiromagno/ensemblr documentation built on Oct. 19, 2023, 11:12 a.m.