VarfromPDB (version 2.2.10)

pheno_extract_HPO: Extract the genes related to a disease or disease alias from HPO database.

Description

Extract the genes associated to a disease or disease alias from the Human Phenotype Ontology (HPO) database. The keyword can also be a clinical feature. All the genes and alias of a disease here can be considered in other databases, including Ophanet, OMIM, ClinVar and Uniprot.

Usage

pheno_extract_HPO(keyword, localPDB.path = paste(getwd(),"localPDB",sep="/"))

Arguments

keyword

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

localPDB.path

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

Value

A list contains two complements

HPO

subset of HPO

diseases_to_genes

extract the genes and alias for a disease(phenotype), or a clinical feature.

Details

Many genetic diseases have multiple aliases, and for a clinical feature, there are many different disease names too. All he information can be gotten from HPO. More details about HPO, please see http://www.human-phenotype-ontology.org/.

The HPO files include phenotype_annotation.tab and diseases_to_genes, which can be downloaded automatically. However, the speed may depend on the network environment. So, we recommend to make the files ready locally before the jobs using localPDB().

References

1.Sebastian K?hler, Sandra C Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data Nucl. Acids Res. (1 January 2014) 42 (D1): D966-D974 doi:10.1093/nar/gkt1026

See Also

extract_omim, extract_uniprot, extract_genes_orphanet, extract_clinvar

Examples

# NOT RUN {
#extract the phenotypes and genes from HPO
#    HPO.phenotype = pheno_extract_HPO("retinoblastoma")
# }