applyDeformationError {simulatorAPMS}R Documentation

Function to calculate the Deformation Errors of AP-MS

Description

The applyDeformationError function simulates FN outputs for those proteins that might have been deformed during the baiting process. The parameters for the function implicitly define which protein, P, is deformed, since the foundPrey is the set of proteins in the ISI which all interact with P. The rateDeform is the rate at which the deformation causes P to accumulate FN's. The return value are those proteins which will become the deformation FN set for protein P in the simulated error model.

Usage

applyDeformationError(foundPrey, rateDeform)

Arguments

foundPrey a vector of proteins that interact with protein P in the ISI; protein P is the protein that has been deformed.
rateDeform a rate at which the deoformed protein P will record FN outputs in the experiment

Details

This is essentially a function for recording more FN interactions among baits and prey. The function takes in a bait that is known to have some deformation as a result of the experimentation.

In essence, the bait loses some capacity to pull other proteins with which it would normally interact.

Value

The return value missedPrey is a vector which is a subset of the vector foundPrey. This subset will be the proteins which will be included as the FN's due to deformation of protein P.

Author(s)

Tony Chiang

See Also

applyFNErrors, \code{runSimulators}

Examples


library(simulatorAPMS)
data(TSNMatrix)
exampleFoundPrey <- rownames(TSNMatrix)[1:50]
applyDeformationError(exampleFoundPrey, 0.5)

  

[Package simulatorAPMS version 1.2.1 Index]