VarfromPDB (version 2.2.10)

genes_compile: Compile the disease-related genes from multiple public databases

Description

To compile a gene set related to a disease especially for a rare disease from multiple databases, including HPO, orphanet, omim, clinvar and uniprot.

Usage

genes_compile(HPO, orphanet, omim, clinvar, uniprot,
       localPDB.path = paste(getwd(),"localPDB",sep="/"))

Arguments

HPO

the object from pheno.extract.HPO function.

orphanet

the object from extract.genes.orphanet function.

omim

the object from extract.omim function.The default value is NULL.

clinvar

the object from extract.clinvar function.

uniprot

the object from extract.uniprot function.

localPDB.path

the path of localized public databases.

Value

A matrix containing the following information

GeneSymbol

gene symbols from HGNC.

chr

chorosomes of the genes.

strand

strands of the genes.

start

start positions (hg19) of the genes.

end

end positions (hg19) of the genes.

EntrezGeneID

Entrez GeneID

ApprovedName

Approved gene name from HGNC.

Synonyms

gene Synonyms.

HPO

the phenotypes from HPO.

Orphanet

the phenotypes from orphanet.

OMIM

the phenotypes from OMIM.

ClinVar

the phenotypes from ClinVar.

Uniprot

the phenotypes from Uniprot.

Details

The relationships between genes and a phenotype in different databases can be intergrated automatically.

See Also

pheno_extract_HPO, extract_omim, extract_genes_orphanet, extract_clinvar, extract_uniprot

Examples

# NOT RUN {
## compile the gene-disease relationship from multiple databases
#genesPDB <- genes_compile(HPO = HPO.Joubert, orphanet = orphanet.joubert,
#                          omim = genes.omim,
#                          clinvar = genes.clinvar,
#                          uniprot = genes.uniprot)
# }