MIRIAM: MIRIAM annotation attributes

In ahmohamed/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

MIRIAM annotation attributes

Description

These functions deals with conforming with MIRIAM annotation guidelines, conversion and mapping between MIRIAM identifiers.

Usage

stdAttrNames(graph, return.value = c("matches", "graph"))

fetchAttribute(
  graph,
  organism = "Homo sapiens",
  target.attr,
  source.attr,
  bridge.web = NPMdefaults("bridge.web")
)

Arguments

graph	An annotated igraph object.
return.value	Specify whether to return the names of matched standard annotations, or modify the graph attribute names to match the standards.
organism	The latin name of the organism (Case-sensitive).
target.attr	The target annotation, given as MIRIAM standard in the format miriam.xxx
source.attr	The source annotation attribute from graph
bridge.web	The base URL for Brigde Database webservices.

Value

For stdAttrNames, matches gives the original attribute names and their MIRIAM version. Since this is done by simple text matching, mismatches may occur for ambiguous annotations (such as GO, EC number). graph returns the input graph with attribute names standardized.

For fetchAttribute, the input graph with the fetched attribute mapped to vertices.

Author(s)

Ahmed Mohamed

See Also

Other Attribute handling methods: getAttrStatus()

Examples

 data(ex_kgml_sig)	# Ras and chemokine signaling pathways in human
 ## Modify attribute names to match MIRIAM standard annotations.
 graph <- stdAttrNames(ex_kgml_sig, "graph")

 # Use Attribute fetcher to get affymetrix probeset IDs for network vertices.
 ## Not run: 
   graph <- fetchAttribute(graph, organism="Homo sapiens",
                   target.attr="miriam.affy.probeset")
 
## End(Not run)

ahmohamed/NetPathMiner documentation built on Nov. 30, 2024, 1:18 a.m.