assessSymmetry: A function that calcualtes some directed degree statistics on...

In Bioconductor/ppiStats: Protein-Protein Interaction Statistical Package

Description

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

Usage

assessSymmetry(bpMat, bpGraph = FALSE,
  prob=0.5, pLevels = 1e-4)

Arguments

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.

Value

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

Author(s)

W Huber

Examples

data("Ito2001BPGraph", package = "ppiData")
assessSymmetry(Ito2001BPGraph, bpGraph=TRUE)

Bioconductor/ppiStats documentation built on Nov. 1, 2021, 1:24 a.m.