edgeTest {gcExplorer} | R Documentation |
Perform a functional relevance test on the edges of a neighborhood graph
edgeTest(object, min.size = 1, group, N = 500, filt = 0.1, useNH = TRUE)
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? |
A matrix giving the cluster sizes, the difference in proportions and the corresponding p-value for each edge considered.
Theresa Scharl
Group2Cluster
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)