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

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

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.

Details

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

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.

Author(s)

Zongfu Cao ([e-mail])

See Also

pheno_extract_HPO, extract_omim, extract_genes_orphanet, extract_clinvar, extract_uniprot

Examples

## 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)

Example output

Loading required package: XML
Loading required package: XML2R
Loading required package: curl
Loading required package: stringr

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