extract_genes_orphanet: Extract the genes related to a genetic disorder from Orphanet

In VarfromPDB: Disease-Gene-Variant Relations Mining from the Public Databases and Literature

Description

extract_genes_orphanet extracts the genes associated to a known genetic disorder or a clinical feature from Orphanet database. The alias of a disease/phenotye are considered based on HPO database and then capture the information in Orphanet.

Usage

extract_genes_orphanet(keyword, 
          localPDB = paste(getwd(),"localPDB",sep="/"), HPO.disease = NULL)

Arguments

keyword	character string: keyword, to search the disease, clinical feature, or phenotype.
localPDB	the path of localized public data bases. The default value is set in the working directory.
HPO.disease	Orpha Number of the disease. The default value is NULL, which means that all the Orpha Numbers of the disease in HPO are added.

Details

The function extracts the genes associated to a genetic disease especial rare disease, or a clinical feature or phenotype from Orphanet database. The keyword is searched not only in Ophanet, but also in HPO considering the alias of the diesease. More details about Ophanet can be seen in http://www.orpha.net/consor/cgi-bin/index.php.

Value

a matrix will be returned including

1.OrphaNumber

2.Phenotype

3.GeneSymbol

4.GeneName

5.GeneType

6.AssociationType

7.AssociationStatus

Author(s)

Zongfu Cao ([e-mail])

References

1.Orphanet: an online rare disease and orphan drug data base. INSERM 1997. Available on http://www.orpha.net. Accessed [date accessed].

2.Orphadata: Free access data from Orphanet. INSERM 1997. Available on http://www.orphadata.org. Data version [XML]

See Also

pheno_extract_HPO, extract_omim, extract_uniprot, extract_clinvar

Examples

    ## extract genes from Orphanet
#    orphanet.phenotype = extract_genes_orphanet(keyword = "retinoblastoma")
 

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