ppiInteraction: Test the association between AP-MS data and phenotype

In PCpheno: Phenotypes and cellular organizational units

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)

PCpheno documentation built on Nov. 8, 2020, 5:10 p.m.