searchBeid: Search a BEID

In patzaw/BED: Biological Entity Dictionary (BED)

Search a BEID

Description

Search a BEID

Usage

searchBeid(x, maxHits = 75, clean_id_search = TRUE, clean_name_search = TRUE)

Arguments

x	a character value to search
maxHits	maximum number of raw hits to return
clean_id_search	clean x to avoid error during ID search. Default: TRUE. Set it to false if you're sure of your lucene query.
clean_name_search	clean x to avoid error during ID search. Default: TRUE. Set it to false if you're sure of your lucene query.

Value

NULL if there is not any match or a data.frame with the following columns:

• value: the matching term

• from: the type of the matched term (e.g. BESymbol, GeneID...)

• be: the matching biological entity (BE)

• beid: the BE identifier

• source: the BEID reference database

• preferred: TRUE if the BEID is considered as a preferred identifier

• symbol: BEID canonical symbol

• name: BEID name

• entity: technical BE identifier

• GeneID: Corresponding gene identifier

• Gene_source: Gene ID database

• preferred_gene: TRUE if the GeneID is considered as a preferred identifier

• Gene_symbol: Gene symbol

• Gene_name: Gene name

• Gene_entity: technical gene identifier

• organism: gene organism (scientific name)

• score: score of the fuzzy search

• included: is the search term fully included in the value

• exact: is the value an exact match of the term

patzaw/BED documentation built on Dec. 13, 2024, 4:29 a.m.