applyFPErrors {simulatorAPMS}R Documentation

Function to calculate FP Errors in AP-MS

Description

The applyFPErrors is a function that simulates a random uniform FP outputs for all bait proteins used in the AP-MS experiementation. For each bait B, notFoundProt is the set of proteins in the ISI that does not have co-membership with B. The parameter rateFP is the rate by which the AP-MS experiment records FP interactions. The rateFP is estimated by the technologies stochastic nature.

Usage

applyFPErrors(notFoundProt, rateFP)

Arguments

notFoundProt A vector of proteins that does not share any co-membership with bait B in the ISI
rateFP The rate at which FP interactions are recorded in the AP-MS experimentation

Details

During the AP-MS wet-lab experiments, a certain rate of proteins that are said to not have co-membership are in fact false postive recordings. This function attempts to simulate the fact that this technology will record interactions that are not present in the ISI.

Value

The proteinsFP is a vector consisting of a subset of the notFoundProt proteins which will serve as the FP output for bait B

Author(s)

Tony Chiang

See Also

applyFNErrors, applyStickyError

Examples


library(simulatorAPMS)
data(TSNMatrix)
exampleNotFoundPrey <- rownames(TSNMatrix)[50:100]
applyFPErrors(exampleNotFoundPrey, 0.04)
  

[Package simulatorAPMS version 1.2.1 Index]