applyFPErrors {simulatorAPMS} | R Documentation |
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.
applyFPErrors(notFoundProt, rateFP)
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 |
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.
The proteinsFP is a vector consisting of a subset of the notFoundProt proteins which will serve as the FP output for bait B
Tony Chiang
applyFNErrors
, applyStickyError
library(simulatorAPMS) data(TSNMatrix) exampleNotFoundPrey <- rownames(TSNMatrix)[50:100] applyFPErrors(exampleNotFoundPrey, 0.04)