ppiStats (version 1.36.0)

estErrProbMethodOfMoments: Estimate false positive and false negative error probabilities by method moments.

Description

Estimate false positive and false negative error probabilities by method moments.

Usage

estErrProbMethodOfMoments(nint, nrec, nunr, ntot)

Arguments

nint

Integer vector. True number of interactions. Typically, the function is called for a range of these, returning all possible solutions for that range.

nrec

Integer scalar. Observed number of reciprocated edges.

nunr

Integer scalar. Observed number of unreciprocated edges.

ntot

Integer scalar. Number of proteins which were tested twice (e.g. both as viable bait and as viable prey).

Value

Matrix with 5 columns nint (a copy of the input argument), pfp1, pfn1, pfp2 and pfn2, and as many rows as the length of nint.

Details

The model is described in the vignette Stochastic and systematic errors in PPI data, by looking at unreciprocated in- or out-edges by W. Huber, T. Chiang and R. Gentleman.

Examples

est = estErrProbMethodOfMoments(nint=seq(8000, 40000, by=100), nrec=9722, nunr=15856, ntot=2000)
if(interactive()) {
  plot(est[, c("pfp2", "pfn2")], type="l", col="blue", lwd=2,
       xlab=expression(p[FP]), ylab=expression(p[FN]))
  abline(h=0, v=0, lty=2)
}