applyDeformationError {simulatorAPMS}R Documentation

Function that handles deformed bait proteins

Description

This function simulates False Negative (FN) observations on those bait proteins known to have been deformed during the AP-MS process.

Usage

applyDeformationError(foundPrey, rateDeform)

Arguments

foundPrey A character vector of proteins names that interact with the a particular deformed protein P
rateDeform The rate at which the deformation in P produces false negative observations within the AP-MS technology

Details

If there is a non-trivial number of deformed bait proteins, the function runSimulators calls the intermediary function simulatorD. This latter function controls applyDeformationError by examining the arguments and parameters. For each deformed bait, simulatorD calls this function to generate deformation errors.

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 character vector, missedPrey:
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 FN observations due to the systematic errors via the deformation of protein P.

Author(s)

T. Chiang

See Also

applyFNErrors, \code{runSimulators}

Examples

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

[Package simulatorAPMS version 1.8.0 Index]