xSubneterGenesMST: Function to identify a minimum spanning tree for subnetworks

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

Function to identify a minimum spanning tree for subnetworks

Description

xSubneterGenesAdv is supposed to identify a minimum spanning tree for subnetworks. It returns an object of class "igraph".

Usage

xSubneterGenesMST(isubg, metric = c("hybrid", "max", "jaccard"),
verbose = T)

Arguments

isubg	an "iSubg" object resulting from xSubneterGenesAdv
metric	the distance metric for subnetworks. It can be either "max" for the maximum distance between any two nodes (one from a subnetwork, and other from another subnetwork) based on the whole network, or "jaccard" for jaccard distance between two subnetworks (nodes overlapped), or "hybrid" (that is, "max" multiplied by "jaccard")
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

a minimum spanning tree, an object of class "igraph". It has graph attributes ('summary', 'detail' and 'matrix'), and node attributes ('xcoord', 'ycoord', 'num_nodes', 'num_edges', 'weight' and 'weight_scaled' [1,5] for visualisation).

See Also

xSubneterGenesAdv

Examples

## Not run: 
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

# a) provide the input nodes/genes with the significance info
## load human genes
org.Hs.eg <- xRDataLoader(RData='org.Hs.eg',
RData.location=RData.location)
sig <- rbeta(500, shape1=0.5, shape2=1)
data <- data.frame(symbols=org.Hs.eg$gene_info$Symbol[1:500], sig)

# b) find a series of maximum-scoring subnets with the desired node number=50
isubg <- xSubneterGenesAdv(data=data, network="STRING_high",
subnet.size=50, RData.location=RData.location)

# c) represent a series of subnets as a minimum spanning tree
mst <- xSubneterGenesMST(isubg)
mst$summary
head(mst$detail)
head(mst$matrix)
gp_mst <- xGGnetwork(mst, node.label='name', node.label.size=3,
node.label.force=1, node.xcoord='xcoord', node.ycoord='ycoord',
edge.size='weight_scaled', node.size='num_edges', node.size.title="Num
of \nedges", node.size.range=c(1,4))

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.