applyDeformationError {simulatorAPMS} | R Documentation |
This function simulates False Negative (FN) observations on those bait proteins known to have been deformed during the AP-MS process.
applyDeformationError(foundPrey, rateDeform)
foundPrey |
A character vector of proteins names that interact with the a particular deformed protein P |
rateDeform |
The rate at which the deformation in P produces false negative observations within the AP-MS technology |
If there is a non-trivial number of deformed bait proteins, the
function runSimulators
calls the intermediary function
simulatorD
. This latter function controls
applyDeformationError
by examining the arguments and
parameters. For each deformed bait, simulatorD
calls
this function to generate deformation errors.
This is essentially a function for recording more FN interactions among baits and prey. The function takes in a bait that is known to have some deformation as a result of the experimentation.
In essence, the bait loses some capacity to pull other proteins with which it would normally interact.
The character vector, missedPrey:
The return value missedPrey is a vector which is a subset of the
vector foundPrey. This subset will be the proteins which will be
included as FN observations due to the systematic errors via the
deformation of protein P.
T. Chiang
applyFNErrors, \code{runSimulators}
data(TSNMatrix) exampleFoundPrey <- rownames(TSNMatrix)[1:50] applyDeformationError(exampleFoundPrey, 0.5)