simulatorD {simulatorAPMS}R Documentation

Function that simulates deformation errors

Description

The simulatorD function is the function that operates on deformed baits. It takes in a vector of deformed baits, and for each bait B, it finds all the proteins interacting with it in the ISI. When it has calculated this set of proteins, it calls the applyDeformationErrors function and gets the subset of proteins as the FN hits. It changes these interactions from 1 to 0 in the PPCM matrix creating the error model.

Usage

simulatorD(deformedBaits, rateD, TSNMat, exMat)

Arguments

deformedBaits Vector of deformed baits
rateD Either a single rate or a vector of rates which the experiment will record FN's
TSNMat The PPCM matrix
exMat The experimental matrix that carries the FN/FP

Details

One interesting aspect of this function is that the rateD can either be a vector of the same length as the vector of deformed baits, or it can be a single rate which is applied to all the deformed baits. The function uses each rate to decide how deformed the bait has become and will create FN observations based on this data.

Value

The return value of this function is an PPCM matrix with error to reflect the FN's that have been induced by applyDeformationErrors

Author(s)

Tony Chiang

See Also

applyDeformationError

Examples


library(apComplex)
data(MBMEcHMSPCI)
data(HMSPCI)
vBaits = rownames(HMSPCI)[1:10]
PPI = MBMEcHMSPCI 
mode(PPI) = "logical"
mode(PPI) = "numeric"
exMat = PPI[vBaits,]
deformedBaits = vBaits[3]
rateD = 0.9
test = simulatorD(deformedBaits, rateD, MBMEcHMSPCI, exMat) 
test[3,]


[Package simulatorAPMS version 1.8.0 Index]