xCombineNet: Function to combine networks from a list of igraph objects

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

xCombineNet is supposed to combine networks from a list of igraph objects.

Usage

xCombineNet(
list_ig,
combineBy = c("union", "intersect"),
attrBy = c("intersect", "union"),
keep.all.vertices = FALSE,
verbose = TRUE
)

Arguments

list_ig	a list of "igraph" objects or a "igraph" object
combineBy	how to resolve edges from a list of "igraph" objects. It can be "intersect" for intersecting edges and "union" for unionising edges (by default)
attrBy	the method used to extract node attributes. It can be "intersect" for intersecting node attributes (by default) and "union" for unionising node attributes
keep.all.vertices	logical to indicate whether all nodes are kept when intersecting edges. By default, it sets to false
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

an object of class "igraph"

Note

none

See Also

xDefineNet

Examples

## Not run: 
# Load the library
library(XGR)

## End(Not run)

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
g1 <- xDefineNet(network="KEGG_environmental",
RData.location=RData.location)
g2 <- xDefineNet(network="KEGG_organismal",
RData.location=RData.location)
ls_ig <- list(g1, g2)
ig <- xCombineNet(ls_ig, combineBy='union', attrBy="intersect",
verbose=TRUE)

## End(Not run)

XGR documentation built on Jan. 8, 2020, 5:06 p.m.