ppiInteract {PCpheno}R Documentation

Test the association between AP-MS data and phenotype

Description

Test the association between AP-MS data and phenotype data via a graph and permutation model.

Usage

ppiInteract(genename, expGraph, bait, prey, perm=10)

Arguments

genename Genes associated to a phenotype
expGraph A graphNEL object (a direct graph instance of classgraph). The nodes are the union of viable baits (VB) and viable prey (VP) of the experiment (see package ScISI)
bait Proteins which was sampled as a bait in the binary relationship
prey Proteins which was sampled as a prey in the binary relationship
perm Number of permutation

Value

The returned value is a list:

Observed Observed values
Expected Expected values after each permutation

Author(s)

R. Gentleman and N. LeMeur

See Also

ScISI

Examples

data(ScISI)
data(essglist)
s1 <- ppiInteract(names(essglist), Gavin2002BPGraph, viableBaits[[8]],
       viablePrey[[8]], perm=10)

[Package PCpheno version 1.4.1 Index]