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

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Description

extract_omim extracts the genes and variants related to a known genetic disorder or a clinical feature from NCBI OMIM database.The alias of a disease/phenotype are caputured from HPO database and searched in OMIM. Furtherly, the variants on a use-defined gene list can be captured meanwhile.

Usage

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extract_omim(keyword, omim.apiKey,  
             localPDB.path = paste(getwd(),"localPDB",sep="/"), 
             type = "both", HPO.disease = NULL, genelist = NULL)

Arguments

keyword

character string: keyword, to search the disease, clinical feature, or phenotype.

omim.apiKey

the API key of OMIM.

localPDB.path

the path of localized public data bases. The default value is set in the working directory.

type

the type of the information to extract, must be one of "gene", "variant", "both"(default).

HPO.disease

MIM number of the disease. The default value is NULL, which means that all the MIM number of the disease in HPO are added.

genelist

the gene(s) related to the disease, or the genes you are interested.

Details

extract_omim extracts the genes from OMIM first, and then translate to appoved gene symbol by HGNC. Then the variants are captured for each gene from OMIM API. However, you should apply for an account and an API key from OMIM.

We recommend to make the files ready locally before a job, in order to avoid a possible failure by the bad network environment.

Value

A list containing two components:

morbidmap

the subset of the file morbidmap, which include all the information about genes and phenotypes in OMIM.

mutations

all the mutations in the genes in OMIM.

Author(s)

Zongfu Cao (caozongfu@gmail.com)

References

1.OMIM:http://www.omim.org/

2.Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. OMIM.org: Online Mendelian Inheritance in Man (OMIM), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 2015 Jan;43(Database issue):D789-98. doi: 10.1093/nar/gku1205. Epub 2014 Nov 26. PubMed PMID: 25428349; PubMed Central PMCID: PMC4383985.

See Also

pheno_extract_HPO, extract_uniprot, extract_genes_orphanet, extract_clinvar

Examples

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## extract genes and variants from OMIM
#    omim.phenotype = extract_omim(keyword= "retinoblastoma",
#                                omim.apiKey = "862D320C6D63C094582A65A54F44B09A0314FC23")