degreeEstimates(m,pTP,pFP)
findDegree(rd,ud,pTP,pFP,N)
degreePMF(deltahat,rd,ud,pTP,pFP,N)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.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.
findDegree(rd=2,ud=2,pTP=0.75,pFP=0.001,N=1000)
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