Find Biological Entity in BED based on their IDs, symbols and names
Usage
findBe(
be = NULL,
organism = NULL,
ncharSymb = 4,
ncharName = 8,
restricted = TRUE,
by = 20,
exclude = c("BEDTech_gene", "BEDTech_transcript")
)Arguments
- 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.
- restricted
boolean indicating if the results should be restricted to current version of to BEID db. If FALSE former BEID are also returned: Depending on history it can take a very long time to return a very large result!
- by
number of found items to be converted into relevant IDs.
- exclude
database to exclude from possible selection. Used to filter out technical database names such as "BEDTech_gene" and "BEDTech_transcript" used to manage orphan IDs (not linked to any gene based on information taken from sources)
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
Relevant ID: the seeked element id
Symbol: the symbol(s) of the corresponding gene(s)
Name: the symbol(s) of the corresponding gene(s)
Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: `attr(x, "scope")“