getNihQuery: create initial NIH Query

In biscuit13161/UNGeneAnno: Collate Gene Annotation Data from Uniprot and NIH Gene Databases

Description

getNihQuery contacts the NIH E-utilities and carries out an initial data query. Accessing the NCBI NIH databases is a two stage process; the getNihQuery function carries out the first stage, returning a short list of IDs and a unique query key. This Query key is then used in the second stage to fetch the results of the query.

Usage

getNihQuery(x, db, query)

## S4 method for signature 'query'
getNihQuery(x, db, query)

Arguments

x	query object.
db	The name of the NCBI database to be searched for the query, e.g. "gene" or "pubmed"
query	The query string for the database

Value

query object a copy of the input object 'x', having the query specifiers from NIH added.

Methods (by class)

• query: query object a copy of the input object 'x', having the query specifiers from NIH added.

See Also

http://www.ncbi.nlm.nih.gov/books/NBK25500/

Examples

f <- query()
slot(f,"gene") <- "BRAF"
db <- "gene"
f <- getNihQuery(f,db,slot(f,"gene"))

biscuit13161/UNGeneAnno documentation built on May 26, 2019, 2:33 a.m.