listInstances: Lists all instances that conform to the selection criteria.

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

Description

Lists all instances that conform to the selection criteria. In contrast to selectInstances this function returns an easier to read list. This function returns an ordered data.table of class, id and name of the instances. Selection criteria are wether instances belong to a certain class or have the specified id or name. Setting a criteria to NULL ignores this criteria. If includeSubClasses is set to TRUE the class criteria is broadened to include all classes that inherit from the given class, e.g. if class="control" and includeSubClasses=TRUE the function will select catalyses and modulations too, since they are a subclass of class control.

Usage

listInstances(
  biopax,
  id = NULL,
  class = NULL,
  name = NULL,
  includeSubClasses = FALSE,
  returnIDonly = FALSE,
  biopaxlevel = 3
)

Arguments

biopax	A biopax model
id	string. ID of the instances to select
class	string. Class of the instances to select
name	string. Name of the instances to select
includeSubClasses	logical. If includeSubClasses is set to TRUE the class criteria is broadened to include all classes that inherit from the given class
returnIDonly	logical. If TRUE only IDs of the components are returned. This saves time for looking up names for every single ID.
biopaxlevel	integer. Set the biopax level here if you supply a data.table directly.

Value

Returns a data.frame containing all instances conforming to the given selection criteria. If returnIDonly=TRUE, only the selector for the internal data.table otherwise.

Author(s)

Frank Kramer

Examples

 # load data
 data(biopaxexample)
 # list all instances of class "protein"
 listInstances(biopax, class="protein")
 # list all instances of class "pathway"
 listInstances(biopax, class="pathway")
 # list all interaction including all subclasses of interactions
 listInstances(biopax, class="interaction", includeSubClasses=TRUE)

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