path: Pathway related queries

In VonWebEinstein/ReactomeAPI:

Description

The rtLowerPathway function traverses the event hierarchy and retrieves the list of all lower level pathways that have a diagram(optional) and contain any form (optional) of the given PhysicalEntity or Event. The rtTopPathway function retrieves the list of top level pathways for the given species.

Usage

rtLowerPathway(id, species = "48887", allForms = TRUE, withDiagram = TRUE,
  silent = FALSE)

rtTopPathway(species, silent = FALSE)

Arguments

id	string. The entity (in any of its forms) or a identifier that has to be present in the pathways.
species	string.The species for which the pathways are requested (SpeciesName or SpeciesTaxId)
allForms	logical;if TRUE, any form of the given PhysicalEntity or Event is consideried. default = TRUE
withDiagram	logical;if TRUE, only those pathways with a diagram will be listed. default = false.
silent	logical; if TRUE, error message will not be printed. default = fasle

Value

a data frame

Examples

 # find  lower level pathways with a diagram, considering all forms of R-HSA-199420
res.1 = rtLowerPathway(id = "R-HSA-199420", species = "48887",
                  allForms = TRUE, withDiagram = TRUE)
# all those pathways with or without a diagram
res.2 =  rtLowerPathway(id = "R-HSA-199420", species = "48887",
                  allForms = TRUE, withDiagram = FALSE)
# search with a known  identifier
res.3 =  rtLowerPathway(id = "PTEN", species = "48887",
                  allForms = TRUE, withDiagram = TRUE)
# find all top level pathways for Homo sapiens
human.1 = rtTopPathway(species = "9606")
# SpeciesName is also permitted for rtTopPath
human.2 = rtTopPathway(species = "Homo sapiens")

VonWebEinstein/ReactomeAPI documentation built on May 9, 2019, 10:02 p.m.