findBe {BED}

Find Biological Entity

Description

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")“