estErrProbMethodOfMoments: Estimate false positive and false negative error...
In Bioconductor/ppiStats: Protein-Protein Interaction Statistical Package

Description Usage Arguments Details Value Author(s) Examples

View source: R/estErrProbMethodOfMoments.R

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

1	estErrProbMethodOfMoments(nint, nrec, nunr, ntot)

`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).

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.

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.

Wolfgang Huber http://www.ebi.ac.uk/huber

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)
}