PCpheno (version 1.32.0)

ppiInteract: 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

See Also

ScISI

Examples

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