Find Biological Entity in BED based on their IDs, symbols and names
findBe(
be = NULL,
organism = NULL,
ncharSymb = 4,
ncharName = 8,
restricted = TRUE,
by = 20,
exclude = c("BEDTech_gene", "BEDTech_transcript")
)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")``
optional. If provided the search is focused on provided BEs.
optional. If provided the search is focused on provided organisms.
The minimum number of characters in searched to consider incomplete symbol matches.
The minimum number of characters in searched to consider incomplete name matches.
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!
number of found items to be converted into relevant IDs.
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)