paxtoolsr (version 1.6.3)

extractIds: Extract IDs from an Extended SIF

Description

Extract IDs from an Extended SIF

Usage

extractIds(nodes, participantType = "ProteinReference",
  idType = "hgnc symbol")

Arguments

nodes

extended SIF nodes entries as a data.table (from convertToDT)

participantType

a vector of types of participants to search; useful to only search protein (ProteinReference) or small molecule (SmallMoleculeReference) related entries.

idType

the type of ID to search for; case-insensitive

Value

• a named vector of the first matches for the given ID type

concept

paxtoolsr

Details

IMPORTANT: Only the first matching ID will be returned. In some cases, multiple IDs will exist.

Examples

tmp <- readSifnx(system.file("extdata", "test_sifnx.txt", package="paxtoolsr"))
results <- extractIds(tmp$nodes)