ppiInteract {PCpheno} | R Documentation |
Test the association between AP-MS data and phenotype data via a graph and permutation model.
ppiInteract(genename, expGraph, bait, prey, perm=10)
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 |
The returned value is a list:
Observed |
Observed values |
Expected |
Expected values after each permutation |
R. Gentleman and N. LeMeur
ScISI
data(ScISI) data(essglist) s1 <- ppiInteract(names(essglist), Gavin2002BPGraph, viableBaits[[8]], viablePrey[[8]], perm=10)