simulator {simulatorAPMS}R Documentation

Function sets up inputs to call all FN/FP errors on the PPCM

Description

For each bait, the simulator function first partitions all the proteins into two groups: (1) those that share co-membership with the bait in the ISI and (2) those that do not. From the first group, simulator calls the function applyFNErrors to generate the FN's for the error model; it calls applyFPErrors on the second group.

Usage

simulator(TSNMat, exMat, bait, rateFP, rateFN)

Arguments

TSNMat The PPCM matrix
exMat The error model matrix
bait A bait protein used in the simulated experiment
rateFP The rate for which FP's are seen in the experiment
rateFN The rate for which FN's are seen in the experiment

Details

See description

Value

The return value is an directed graph matrix of PPCM with the embedded FN/FP's incorporated.

Author(s)

Tony Chiang

See Also

runSimulators

Examples


library(simulatorAPMS)
data(simEX)
data(vBaitsEX)
PPCM = simEX 
mode(PPCM) = "logical"
mode(PPCM) = "numeric"
estMat = PPCM[vBaitsEX,]
rateFP = 0.025
rateFN = 0.20
simulator(simEX, estMat, vBaitsEX[2], rateFP, rateFN)[2,]


[Package simulatorAPMS version 1.2.1 Index]