DEPRECATED: use searchBeid and geneIDsToAllScopes instead. This function is meant to be used with getRelevantIds in order to implement a dictonary of identifiers of interest. First the searchId function is used to search a term. Then the getRelevantIds function is used to find the corresponding ID in a context of interest.
Usage
searchId(
searched,
be = NULL,
organism = NULL,
ncharSymb = 4,
ncharName = 8,
verbose = FALSE
)Arguments
- searched
the searched term. Identifiers are searched by exact match. Symbols and names are also searched for partial match when searched is greater than ncharSymb and ncharName respectively.
- be
optional. If provided the search is focused on provided BEs.
- organism
optional. If provided the search is focused on provided organisms.
- ncharSymb
The minimum number of characters in searched to consider incomplete symbol matches.
- ncharName
The minimum number of characters in searched to consider incomplete name matches.
- verbose
boolean indicating if the CQL queries should be displayed
Value
A data frame with the following fields:
found: the element found in BED corresponding to the searched term
be: the type of the element
source: the source of the element
organism: the related organism
entity: the related entity internal ID
ebe: the BE of the related entity
canonical: if the symbol is canonical
gene: list of the related genes BE internal ID
Exact matches are returned first folowed by the shortest elements.