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

Description Usage Arguments Details Value Author(s) Examples

View source: R/nullDistDoublyTestedEdges.R

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

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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

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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="="))
  }

ppiStats documentation built on May 31, 2017, 2:55 p.m.

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