GSNA (version 0.1.4.2)

gsnToIgraph: gsnToIgraph

Description

For a GSNData object containing an edge list, generate an igraph object.

Usage

gsnToIgraph(object, distance = NULL)

Value

Returns an igraph object corresponding to the edges and vertices in the GSNData

object's edge-list data.frame.

Arguments

object

A GSNData object containing a pared distance matrix and an edge list.

distance

(optional) A character vector specifying a distance to use. If no distance is specified, the value of the default_distance will be used.

Details

This is used by gsnPlotNetwork to generate an igraph. Users will probably not need to call gsnToIgraph, for most cases. If edges are not found, it will emit an error.

See Also

gsnPlotNetwork() plot.GSNData()

Examples

library(GSNA)

# In this example, we generate a gene set network from CERNO example
# data. We begin by subsetting the CERNO data for significant results:
sig_pathways.cerno <- subset( Bai_CiHep_DN.cerno, adj.P.Val <= 0.05 )

# Now create a gene set collection containing just the gene sets
# with significant CERNO results, by subsetting Bai_gsc.tmod using
# the gene set IDs as keys:
sig_pathways.tmod <- Bai_gsc.tmod[sig_pathways.cerno$ID]

# And obtain a background gene set from differential expression data:
background_genes <- toupper( rownames( Bai_CiHep_v_Fib2.de ) )

# Build a gene set network:
sig_pathways.GSN <-
   buildGeneSetNetworkJaccard(geneSetCollection = sig_pathways.tmod,
                              ref.background = background_genes )

# Now import the CERNO data:
sig_pathways.GSN <- gsnImportCERNO( sig_pathways.GSN,
                                    pathways_data = sig_pathways.cerno )

# Now we can pare the network and assign subnets:
sig_pathways.GSN <- gsnPareNetGenericHierarchic( object = sig_pathways.GSN )
sig_pathways.GSN <- gsnAssignSubnets( sig_pathways.GSN )

# Now, create an igraph version of the network:
sig_pathways.igraph <- gsnToIgraph( object  = sig_pathways.GSN )

# This can be plotted via igraph::plot.igraph:
plot( sig_pathways.igraph )