searchSubnet {signet}R Documentation

Search for a high scoring subnetwork

Description

A simulated annealing algorithm to find the highest scoring subnetwork within a graph.

Usage

searchSubnet(pathway, scores, iterations = 1000, background)

Arguments

pathway

A gene network, or a list of gene networks, in the graphNEL format.

scores

A data frame with two columns: gene identifiers list (IDs have to be the same as for the pathways, e.g. Entrez) and associated scores.

iterations

Number of iterations.

background

For development purposes.

Value

A signet object or a list of signet objects. Each signet object consists in a table with gene IDs, their state, their score; the subnetwork score and size and the p-value.

Examples


# Get KEGG pathways from the package graphite:
# library(graphite)
# kegg <- pathways("hsapiens", "kegg")
# kegg_human <- lapply(kegg, pathwayGraph)

data(daub13) # load the gene scores from Daub et al. (2013)

#run the search in all the pathways with 2500 iterations (default)
example <- searchSubnet(kegg_human, scores)
summary(example)

[Package signet version 1.2.3 Index]