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

Description Usage Arguments Value Author(s) Examples

View source: R/assessSymmetry.R

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

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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

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library(ppiData)
assessSymmetry(Ito2001BPGraph, bpGraph=TRUE)

ppiStats documentation built on Nov. 8, 2020, 8:18 p.m.