nullDistDoublyTestedEdges: Null distribution of number of reciprocated, unreciprocated...

In Bioconductor/ppiStats: Protein-Protein Interaction Statistical Package

Description

Calculate the null distribution of the number of reciprocated, unreciprocated and missing edges in a stochastic model where each edge is tested twice.

Usage

nullDistDoublyTestedEdges(deltaMax, n, pFP, pFN)

Arguments

deltaMax	Integer. Distributions will be calculated for model parameter delta=0, 1, 2, ..., deltaMax.
n	Integer. The parameter n of the model.
pFP	Numeric. The parameter pFP of the model.
pFN	Numeric. The parameter pFN of the model.

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.

This function can be quite slow, its runtime grows quickly with deltaMax (and is roughly independent of n, pFP, pFN). The example below should take only a few seconds on a reasonable computer, though.

Value

3d array with dimensions nMax+1 x nMax+1 x deltaMax+1 whose element p[nr+1, nu+1, delta+1] is the corresponding joint probability. nMax+1 is calculated (probably too conservatively) by the function to make sure that no probability leaks out of the array.

Author(s)

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

Examples

p = nullDistDoublyTestedEdges(32, 1000, pFP=0.001, pFN=0.15)

if(interactive() && require("RColorBrewer"))
  for(k in 1:dim(p)[3]) {
    image(sqrt(p[,,k]), xlab=expression(N[rec]), ylab=expression(N[unrec]),
        main = expression(P(N[rec], N[unrec]~";"~ delta^"*", n, p[FP], p[FN])),
        x = 1:dim(p)[1], y = 1:dim(p)[2], 
        col = colorRampPalette(brewer.pal(9, "GnBu"))(256))
    text(35, 35, paste("delta", k, sep="="))
  }

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