runSimulators {simulatorAPMS}R Documentation

Function that sets up the ISI et al to run the simulations

Description

The runSimulators function is the primary function for the simulation tool. It first takes in an in the incidence matrix of the silico interactome's (ISI) bipartite graph representation. Since not all the proteins are documented in the ISI, it also appends all proteins found in the organism to the ISI. From there, we derive the Protein-Protein Co-Membership (PPCM) matrix. We then only take the rows indexed by baits, and apply all the simulated errors to this matrix. The result is an error model simulation of an AP-MS experiment.

Usage

runSimulators(TSNMat, vBaits, vDeform, vStky, rateFP, rateFN, rateD, rateS, missedProt, seedIn)

Arguments

TSNMat Incidence Matrix of ISI's bipartite graph representation
vBaits The vector of baits used in the simulated AP-MS experiment
vDeform The vector of deformed baits
vStky The vector of sticky baits
rateFP Rate at which AP-MS returns FP's
rateFN Rate at which AP-MS returns FN's
rateD Rate(s) at which the deformed baits return FN's
rateS Rate(s) at which the sticky baits return FP's
missedProt The vector of proteins that have trivial co-membership and not recorded by the ISI
seedIn Seed used in the random generator which allows the user to set the seed for reproducible experiments

Details

The details of the function are as follows. TSNMat and vBaits have been described. The vStky and vDeformed are baits that account for systematic errors called sticky protein errors and deformed protein error, and the rateS and rateD are the rates for the respective systematic errors. The missedProt are those who are in no protein complex and thus not recorded in the ISI, but needed for simulation.

Value

The return value for this function is a rectangular matrix with rows indexed by the baits and the columns indexed by all proteins in the organism. This matrix will differ from the PPCM matrix in that it will have FN/FP's embedded from the simulated error functions.

Author(s)

Tony Chiang

See Also

simulator

Examples

library(simulatorAPMS)
data(simEX)
data(vBaitsEX)
data(missedProtEX)
runSimulators(simEX, vBaitsEX, vBaitsEX[2], vBaitsEX[3], 0.05, 0.1, 0, 0, missedProtEX, 357)

[Package simulatorAPMS version 1.8.0 Index]