idProteinErrorType: A function to identify those proteins affected by either...

In Bioconductor/ppiStats: Protein-Protein Interaction Statistical Package

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.

Author(s)

T Chiang

References

~put references to the literature/web site here ~

Examples

data("Ito2001BPGraph", package = "ppiData")
data("viableBaits", package = "ppiData")
idSystematic(Ito2001BPGraph, viableBaits[[1]], bpGraph=TRUE)

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