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Check biological entities (BE) identifiers

Source: R/checkBeIds.R
checkBeIds.Rd

This function takes a vector of identifiers and verify if they can be found in the provided source database according to the BE type and the organism of interest. If an ID is in the DB but not linked directly nor indirectly to any entity then it is considered as not found.

Usage

checkBeIds(ids, be, source, organism, stopThr = 1, caseSensitive = FALSE)

Arguments

ids

a vector of identifiers to be checked

be

biological entity. See getBeIds. Guessed if not provided

source

source of the ids. See getBeIds. Guessed if not provided

organism

the organism of interest. See getBeIds. Guessed if not provided

stopThr

proportion of non-recognized IDs above which an error is thrown. Default: 1 ==> no check

caseSensitive

if FALSE (default) the case is not taken into account when checking ids.

Value

invisible(TRUE). Stop if too many (see stopThr parameter) ids are not found. Warning if any id is not found.

See also

getBeIds, listBeIdSources, getAllBeIdSources

Examples

if (FALSE) { # \dontrun{
checkBeIds(
   ids=c("10", "100"), be="Gene", source="EntrezGene", organism="human"
)
checkBeIds(
   ids=c("10", "100"), be="Gene", source="Ens_gene", organism="human"
)
} # }