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

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

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.

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.

Value

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

Author(s)

Zongfu Cao ([e-mail])

See Also

pheno_extract_HPO, extract_omim, extract_genes_orphanet, extract_clinvar, extract_uniprot

Examples

#variantsPDB <- variants_compile(omim = variants.omim, 
#                                clinvar = variants.clinvar,
#                                uniprot = variants.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.