BED (version 1.5.2)

getDirectOrigin: Get the direct origin of BE identifiers

Description

The origin is directly taken as provided by the original database. This function does not return indirect relationships.

Usage

getDirectOrigin(
  ids,
  sources = NULL,
  process = c("is_expressed_as", "is_translated_in", "codes_for")
)

Value

a data.frame with the following columns:

• origin: the origin BE identifiers

• osource: the origin database

• product: the product BE identifiers

• psource: the production database

• canonical: whether the production process is canonical or not

The process is also returned as an attribute of the data.frame.

Arguments

ids

list of product identifiers

sources

a character vector corresponding to the possible product ID sources. If NULL (default), all sources are considered

process

the production process among: "is_expressed_as", "is_translated_in", "codes_for".

See Also

getDirectOrigin, convBeIds

Examples

if (FALSE) {
oriId <- c("XP_016868427", "NP_001308979")
res <- getDirectOrigin(
   ids=oriId,
   source="RefSeq_peptide",
   process="is_translated_in"
)
attr(res, "process")
}