testSubnet: Test the significance of high-scoring subnetworks found using...

Description Usage Arguments Value Examples

View source: R/testSubnet.R

Description

Test the significance of high-scoring subnetworks found using simulated annealing.

Usage

1
testSubnet(sigObj, null)

Arguments

sigObj

A list of signet objects obtained using the searchSubnet function.

null

Vector of null subnetwork scores generated using the nullDist function.

Value

For each signet object, a p-value is computed given the provided emnpirical null distribution.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
# 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)

# generate the null distribution (here, only 5 values, but
# at least 1000 are advised)
null <- nullDist(kegg_human, scores, n = 5)
example <- testSubnet(example, null) #now, 'example' includes p-values
summary(example)

CMPG/signet documentation built on May 13, 2018, 2:31 p.m.