stdAttrNames {NetPathMiner} | R Documentation

## 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)

[Package NetPathMiner version 1.16.0 Index]