VarfromPDB (version 2.2.10)

genes_add_pubmed: Compile the disease-related genes from PubMed abstracts into the gene set from the public databases

Description

To compile the genes related to a disease especially for a rare disease from PubMed abstracts into the gene set from the public databases, including HPO, orphanet, omim, clinvar and uniprot.

Usage

genes_add_pubmed(keyword,genepdb, pubmed, 
             localPDB.path = paste(getwd(), "localPDB", sep = "/"))

Arguments

keyword

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

genepdb

the object from function genes_compiled.

pubmed

the object from function extract_pubmed. The object need to be checked mannually.

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.

pubmed

the phenotypes from PubMed.

Details

The relationships between genes and a phenotype are compared with those from public databases, then the additional relationships can be merged together. For the object from function extract_pubmed maybe have noise, we strongly recommend that the additional relationships between genes and phenotypes should be pay more attention and checked mannually.

See Also

extract_pubmed, genes_compile

Examples

# NOT RUN {
## add the relationships between genes and phenotypes into those from 
## the public databases. 
#geneAll <- genes_add_pubmed(genepdb= genesPDB, pubmed=genes.pubmed)
# }