VarfromPDB (version 2.2.10)

extract_uniprot: Extract the genes and variants related to a genetic disorder from UniprotKB

Description

extract_uniprot extracts the genes and variants associated to a known genetic disorder or a clinical feature from the UniProt Knowledgebase (UniprotKB). The alias of a disease/phenotye are caputured from HPO database. Furtherly, the gene mutations on a gene list can also be captured at the same time.

Usage

extract_uniprot(keyword, localPDB.path = paste(getwd(),"localPDB",sep="/"), 
                HPO.disease = NULL, genelist = NULL)

Arguments

keyword

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

localPDB.path

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

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) associated to the disease, or the genes you are interested.

Value

A list containing two components:

genes.extr

genes captured from Uniprot.

dat.extr

variants captured from Uniprot.

Details

extract_uniprot extracts the genes and variants from Uniprot, which focus on amino acid altering variants, and manually curated Human polymorphisms and disease mutations from UniProtKB/Swiss-Prot.

The Uniprot file humsavar can be downloaded automatically. However, the speed may depend on the network environment. So, we recommend to make the file ready locally before the jobs using localPDB().

References

1.The UniProt Consortium UniProt: a hub for protein information. Nucleic Acids Res. 43: D204-D212 (2015).

See Also

pheno_extract_HPO, extract_omim, extract_genes_orphanet, extract_clinvar

Examples

# NOT RUN {
## extract the genes and variants associated to a known mendelian 
## disorder from uniprot
#    uniprot.phenotype = extract_uniprot(keyword="retinoblastoma")
# }