extract_uniprot: Extract the genes and variants related to a genetic disorder...
In VarfromPDB: Disease-Gene-Variant Relations Mining from the Public Databases and Literature

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1 2	extract_uniprot(keyword, localPDB.path = paste(getwd(),"localPDB",sep="/"), HPO.disease = NULL, genelist = NULL)

`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.

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().

A list containing two components:

`genes.extr`	genes captured from Uniprot.
`dat.extr`	variants captured from Uniprot.

Zongfu Cao (caozongfu@nrifp.org.cn)

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

pheno_extract_HPO, extract_omim, extract_genes_orphanet, extract_clinvar

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## extract the genes and variants associated to a known mendelian 
## disorder from uniprot
#    uniprot.phenotype = extract_uniprot(keyword="retinoblastoma")

VarfromPDB documentation built on May 2, 2019, 2:10 a.m.