applyStickyError {simulatorAPMS}R Documentation

Function that takes sticky proteins and calculates FP's

Description

This function simulates False Positive (FP) observations on those bait proteins known to have affinity towards a large number of prey proteins during the AP-MS process.

Usage

applyStickyError(notFoundProt, rateSticky)

Arguments

notFoundProt A character vector of proteins that have no known interactions with the bait protein B.
rateSticky The rate at which bait B attracts other proteins ands records FP observations due to its systematic affinity to interact with other proteins.

Details

If there is a non-trivial number of sticky bait proteins, the function runSimulators calls the intermediary function simulatorS. This latter function controls applyStickyError by examining the arguments and parameters. For each sticky bait, simulatorS calls this function to generate un-natural interactions.

This is essentially a function for recording more FP interactions among baits and non-prey. The function takes in a bait that is known to have some high level of finding prey as a result of the experimentation.

In essence, the bait attracts and binds to other proteins with which it would normally not interact.

Value

The character vector, ProtInErr:
The return value, ProtInErr, is a vector consisting of a subset of proteins from the set notFoundProt. This subset will be those proteins which form systematic FP observations for the simulation.

Author(s)

T. Chiang

See Also

applyFPErrors, applyDeformationError

Examples

library(simulatorAPMS)
data(TSNMatrix)
exampleNotFoundPrey <- rownames(TSNMatrix)[1:50]
applyStickyError(exampleNotFoundPrey, 0.9)

[Package simulatorAPMS version 1.8.0 Index]