degreeEstimates: Estimate per-node degree in viable bait-prey (VBP) graph...

In Bioconductor/ppiStats: Protein-Protein Interaction Statistical Package

Description

Estimate per-node degree in viable bait-prey (VBP) graph using maximum likelihood.

Usage

degreeEstimates(m,pTP,pFP)
findDegree(rd,ud,pTP,pFP,N)
degreePMF(deltahat,rd,ud,pTP,pFP,N)

Arguments

m	Square incidence matrix for VBP graph.
pTP	True positive probability.
pFP	False positive probability.
rd	Observed number of reciprocated edges.
ud	Observed number of unreciprocated edges.
deltahat	Estimate of node degree.
N	Number of proteins which were tested twice (e.g. both as viable bait and as viable prey.) Should equal the number of rows of m.

Details

degreeEstimates returns per-node degree estimates using the maximum likelihood method of Scholtens et al. (Submitted). It takes arguments m, which is an incidence matrix of bait-prey relationships, typically a VBP graph filtered for proteins prone to systematic bias, as well as pTP and pFP values, globally applicable to the entire graph.

degreeEstimates calls the function findDegree which estimates degree for a single node, given its observed number of reciprocated and unreciprocated incident edges. findDegree takes an argument N which is the number of proteins in the graph that were tested twice. When degreeEstimates calls findDegree, N is set to the first dimension of the incidence matrix m.

degreePMF calculates the value of the pmf for an estimated degree, given observed numbers of reciprocated and unreciprocated edges, as well as pTP, pFP, and N. It is not generally called directly by the user. It is used to locate the maximum likelihood estimator for degree.

Value

degreeEstimates returns a named vector of degree estimates for each node in the graph.

findDegree returns a single degree estimate for one node.

degreePMF returns the value of the pmf for the multinomial model at a specified estimate of node degree, given the number of observed reciprocated and unreciprocated edges incident on the node and pTP and pFP.

Author(s)

Denise Scholtens, [e-mail]

References

Scholtens D, Chiang T, Huber W, Gentleman R. Estimating node degree in bait-prey graphs. (Submitted).

Examples

findDegree(rd=2,ud=2,pTP=0.75,pFP=0.001,N=1000)

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