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)