createIGraphObject: Create graph object from gene interaction list

In bhatturam/prius: Affected pathway ranking in differential gene expression analysis

Description

Convert a data frame containing the gene interaction list into a form usable by the other functions in the library. This is just a wrapper around the igraph graph.edgelist function, which creates and returns an igraph object with a data frame containing the in and outdegrees.

Usage

createIGraphObject(geneInteractions)

Arguments

geneInteractions

- a data frame that contains the gene interaction graph in two columns, the first being the source HGNCSymbol and the second being the target HGNCSymbol of an interaction. See getGeneInteractionsFromReactomeMITAB, getGeneInteractionsFromIRefMITAB for more details

Value

A list containing igraph_object - the igraph object and vertex_map - a frame containing node attributes currently indegree and outdegree

References

http://igraph.org/r/doc/graph_from_edgelist.html

See Also

getGeneInteractionsromReactomeMITAB, getGeneInteractionsFromIRefMITAB

Examples

## Not run: 
     data_folder=tempdir()
     usmap<-getUniProtToHGNCSymbolMapping(data_folder)
     mitab <- downloadReactomeInteractionsMITAB(data_folder)
     geneInteraction <- getGeneInteractionListFromReactomeMITAB(mitab,usmap)
     ppiGraph<-createIGraphObject(geneInteraction)

## End(Not run)

bhatturam/prius documentation built on May 12, 2019, 8:24 p.m.