getEnsemblVariantFeatures: Get features of given variant IDs.

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Get features of given variant IDs.

Description

Function retrieves features for given variant IDs from the Ensembl database. It handles requests asynchronously in batches due to server limits and includes options to fetch additional variant information. Error handling for different HTTP response statuses is implemented to manage request failures.

Usage

getEnsemblVariantFeatures(
  species,
  variant.ids,
  include.genotypes = FALSE,
  include.phenotypes = FALSE,
  include.allele.frequencies = FALSE,
  include.genotype.frequencies = FALSE,
  curl.max.con = 100,
  verbose = 1
)

Arguments

species	Species name or alias (e.g., homo_sapiens, human).
variant.ids	A vector of variant IDs (e.g., rs56116432, COSM476).
include.genotypes	Include genotypes in the response? Default FALSE.
include.phenotypes	Include phenotypes in the response? Default FALSE.
include.allele.frequencies	Include allele frequencies? Default FALSE.
include.genotype.frequencies	Include genotype frequencies? Default FALSE.
curl.max.con	Maximum number of concurrent connections for curl requests. Default is 100.
verbose	Verbosity level: 1 for error only, 2 for all requests. Default 1.

Value

A variant-named list containing lists of variant features.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.