| searchId {BED} | R Documentation |
Search identifier, symbol or name information
Description
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.