applyFNErrors {simulatorAPMS}R Documentation

Function to calculate FN Errors in AP-MS

Description

The applyFNErrors is a function that simulates a random uniform FN outputs for all bait proteins used in the AP-MS experiementation. For each bait B, foundPrey is the set of proteins in the ISI that interacts with B. The parameter rateFN is the rate by which the AP-MS experiment records FN interactions. This FN rate is an estimate based on the stochastic nature of the technology.

Usage

applyFNErrors(foundPrey, rateFN)

Arguments

foundPrey A vector of proteins that interacts with bait B in the TSN
rateFN The rate at which FN interactions are recorded in the AP-MS experiment

Details

During the AP-MS wet-lab experiments, a certain rate of proteins that are said to not interact are in fact false negative recordings. This function attempts to simulate the fact that this technology will fail to be consistent in the bait-prey pull down systems or fail to pull down true co-membership at all.

Value

The proteinsFN is a vector consisting of a subset of the foundPrey proteins which will serve as the FN output for bait B.

Author(s)

Tony Chiang

See Also

applyFPErrors,applyDeformationError

Examples


library(simulatorAPMS)
data(TSNMatrix)
exampleFoundPrey <- rownames(TSNMatrix)[1:50]
applyFNErrors(exampleFoundPrey, 0.3)
  

[Package simulatorAPMS version 1.2.1 Index]