assessSymmetry {ppiStats} | R Documentation

## A function that calcualtes some directed degree statistics on graphs using a binomial error model

### 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

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

[Package ppiStats version 1.46.0 Index]