getXrefAnnotations: This function returns the annotations of the supplied...

In frankkramer-lab/rBiopaxParser: Parses BioPax files and represents them in R

Description

This function returns the annotations of the supplied IDs in a data.table.

Usage

getXrefAnnotations(
  biopax,
  id,
  splitComplexes = FALSE,
  followPhysicalEntityParticipants = TRUE,
  biopaxlevel = 3
)

Arguments

biopax	A biopax model
id	vector of strings. IDs of instances to get annotations
splitComplexes	logical. If TRUE complexes are split up into their components and the annotation of the components is added.
followPhysicalEntityParticipants	logical. If TRUE physicalEntityParticipants are resolved to their corresponding physicalEntities and their annotation is added.
biopaxlevel	integer. Set the biopax level here if you supply a data.table directly.

Value

Returns data.table with annotations

Author(s)

fkramer

Examples

 # load data
 data(biopaxexample)
# example of annotation for a protein:
getXrefAnnotations(biopax, id="ex_m_100647")
# no annotations for exactly the complex
getXrefAnnotations(biopax, id="ex_m_100650")
# split up the complex and get annotations for all the molecules involved
getXrefAnnotations(biopax, id="ex_m_100650", splitComplexes=TRUE)

frankkramer-lab/rBiopaxParser documentation built on July 19, 2020, 9:49 a.m.