getDirectOrigin: Get the direct origin of BE identifiers

In patzaw/BED: Biological Entity Dictionary (BED)

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")
)

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".

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.

See Also

getDirectOrigin, convBeIds

Examples

## Not run: 
oriId <- c("XP_016868427", "NP_001308979")
res <- getDirectOrigin(
   ids=oriId,
   source="RefSeq_peptide",
   process="is_translated_in"
)
attr(res, "process")

## End(Not run)

patzaw/BED documentation built on Dec. 13, 2024, 4:29 a.m.