ppiStats (version 1.38.0)

idProteinErrorType: A function to identify those proteins affected by either stochastic or systematic errors

Description

This function takes in either a bait to prey Graph (matrix) and, based on a binomial error model, partitions proteins identified as either affected by systematic or stochastic error. It is a wrapper function that will eventually call the qbinom function.

Usage

idSystematic(bpMat, viable, bpGraph = FALSE, pThresh = 0.01, pLevels =
1e-4, prob=0.5)
idStochastic(bpMat, bpGraph = FALSE, pThresh = 0.01, pLevels =
1e-4, prob=0.5)

Arguments

bpMat

Either a bait to prey directed graphNEL or its corresponding adjacency matrix.

viable

This is a character vector of viable proteins. It is only used in the idSystematic function.

bpGraph

A logical. If TRUE, than bpMat is passed in by the user as a graphNEL.

pThresh

The p-value threshold for which to partition stochastic or systematic errors

pLevels

A numeric. It gives the levels to calculate the countours of the function in p in the (n-in, n-out)-plane

prob

A numeric. The probability parameter in the call to the qbinom function.

Value

A character vector of proteins either affected by systematic or stochastic errors.

References

~put references to the literature/web site here ~

Examples

library(ppiData)
idSystematic(Ito2001BPGraph, viableBaits[[1]], bpGraph=TRUE)