VarfromPDB (version 2.2.10)

variants_compile: Compile the disease-related variants from multiple public databases

Description

To get a variant set related to a disease especially for a rare disease from multiple database, including omim, clinvar and uniprot.

Usage

variants_compile(omim, clinvar, uniprot, 
     localPDB.path = paste(getwd(), "localPDB", sep = "/"))

Arguments

omim

the object from extract.omim function.

clinvar

the object from extract.clinvar function.

uniprot

the object from extract.uniprot function.

localPDB.path

the path of localized public data bases.

Value

A matrix containing all the variant-gene-phenotypes relationships.

Details

A variant maybe have different names in different databases. All the variants in OMIM and Uniprot are compared with ClinVar, then the additional variants are appended the clinVar-like summary variant set.

See Also

pheno_extract_HPO, extract_omim, extract_genes_orphanet, extract_clinvar, extract_uniprot

Examples

# NOT RUN {
#variantsPDB <- variants_compile(omim = variants.omim, 
#                                clinvar = variants.clinvar,
#                                uniprot = variants.uniprot)
# }