| applyStickyError {simulatorAPMS} | R Documentation |
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.
applyStickyError(notFoundProt, rateSticky)
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. |
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.
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.
T. Chiang
applyFPErrors, applyDeformationError
library(simulatorAPMS) data(TSNMatrix) exampleNotFoundPrey <- rownames(TSNMatrix)[1:50] applyStickyError(exampleNotFoundPrey, 0.9)