MIRIAM annotation attributes

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

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.

See also

Other Attribute handling methods: getAttrStatus()

Author

Ahmed Mohamed

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")
#> This graph was created by an old(er) igraph version.
#> ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
#> For now we convert it on the fly...

 # Use Attribute fetcher to get affymetrix probeset IDs for network vertices.
 if (FALSE) { # \dontrun{
   graph <- fetchAttribute(graph, organism="Homo sapiens",
                   target.attr="miriam.affy.probeset")
 } # }