extract_clinvar_mod: Extract the genes and variants related to a genetic disorder...

In VilainLab/Nanotator: Next generation structural variant annotation and classification

Extract the genes and variants related to a genetic disorder from ClinVar

Description

Extract the genes and variants related to a genetic disorder from ClinVar

Usage

extract_clinvar_mod(
  keyword,
  localPDB.path,
  type = "both",
  HPO.disease = NULL,
  genelist = NULL,
  OMIM = NULL
)

Arguments

keyword	character. character string: keyword, to search a disease, a clinical feature, or a phenotype.
localPDB.path	character. the path of localized public data bases. The default value is set in the working directory.
type	character. the type of the information to extract, must be one of "gene", "variant","both"(default).
HPO.disease	character. MIM number of the disease. The default value is NULL, which means that all the OMIM number of the disease in HPO are added. localized public data bases. The default value is set in the working directory.
genelist	character. the gene(s) associated to the disease, or the genes you are interested.
OMIM	character. whether use the information from OMIM database. The default value is NULL. It can be set 'yes' when you make sue you have a OMIM API key.

Value

subset of the file gene_condition_source_id, which include all the information about genes and phenotypes in ClinVar and subset of the file variant_summary.txt, but added sevetal colomns which describe the phenotype from GeneReview, MedGen, and OMIM databases. Function modified from extract_clinvar function VarFromPDB.

Examples

keyword = "retinoblastoma"
extract_clinvar_mod(keyword,
localPDB.path = system.file("extdata", "localPDB", package="nanotatoR"),
type = "both", HPO.disease = NULL,
genelist = NULL, OMIM = NULL)

VilainLab/Nanotator documentation built on Aug. 2, 2024, 8:45 p.m.