getRelevantIds {BED}

Get relevant IDs for a formerly identified BE in a context of interest

Description

DEPRECATED: use searchBeid and geneIDsToAllScopes instead. This function is meant to be used with searchId 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 IDs in a context of interest.

Usage

getRelevantIds(
  d,
  selected = 1,
  be = c(listBe(), "Probe"),
  source,
  organism,
  restricted = TRUE,
  simplify = TRUE,
  verbose = FALSE
)

Arguments

d

the data.frame returned by searchId.

selected

the rows of interest in d

be

the BE in the context of interest

source

the source of the identifier in the context of interest

organism

the organism in the context of interest

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!

simplify

if TRUE (default) duplicated IDs are removed from the output

verbose

if TRUE, the CQL query is shown

Value

The d data.frame with a new column providing the relevant ID in the context of interest and without the gene field. Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: attr(x, "scope")

See Also

searchId