edgeTest {gcExplorer}R Documentation

Functional Relevance Test

Description

Perform a functional relevance test on the edges of a neighborhood graph

Usage

edgeTest(object, min.size = 1, group, N = 500, filt = 0.1, useNH = TRUE)

Arguments

object An object of class "kccasimple".
min.size Minimum number of grouped genes in a cluster to be considered for testing
group Vector of cluster memberships of functionally grouped genes (from function Group2Cluster).
N Number of permutations.
filt Threshold for edges in the neighborhood graph to be considered for testing.
useNH Use the neighborhood structure or test all combination of nodes?

Value

A matrix giving the cluster sizes, the difference in proportions and the corresponding p-value for each edge considered.

Author(s)

Theresa Scharl

See Also

Group2Cluster

Examples

data("hsod")
data("gobp")
set.seed(1111)
cl1 <- qtclust(hsod, radius = 2, save.data = TRUE)

g1 <- Group2Cluster(cl1, gonr = "GO:0009061", 
        source.group = gobp[,3], source.id=gobp[,1], 
        id = bn_hsod)
test1 = edgeTest(cl1, group=g1, min.size=2, useNH=TRUE, filt=0.1, N=1000)

[Package gcExplorer version 0.9-1 Index]