assessSymmetry {ppiStats} | R Documentation |
This function takes in a bait to prey protein-protein interaction graph (undirected) and calculates the reciprocated degree, the unreciprocated in and out degrees. Using this information and binomial error model, it asses the p-value for the in and out degree of each protein. Lastly, it plots the countour curves for these p-values
assessSymmetry(bpMat, bpGraph = FALSE, prob=0.5, pLevels = 1e-4)
bpMat |
Either a bait to prey directed graphNEL or its corresponding adjacency matrix. |
bpGraph |
A logical. If TRUE, than bpMat is passed in by the user as a graphNEL. |
pLevels |
A numeric vector. It gives the levels to calculate the countours of the function in p in the (n-in, n-out)-plane |
prob |
A numeric. The bias of the coin used in the function pbinom call. |
A list:
deg |
A 3xn matrix. The rows are indexed by each protein. Column one gives the number of reciprocated edges; column two gives the number of unreciprocated out edges; colunm three gives the number of unreciprocated in-edges |
p |
The p-value for each protein with experimental in and out degrees |
countours |
The countours as a function of p |
W Huber
library(ppiData) assessSymmetry(Ito2001BPGraph, bpGraph=TRUE)