simulator {simulatorAPMS} | R Documentation |
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.
simulator(TSNMat, exMat, bait, rateFP, rateFN)
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 |
See description
The return value is an directed graph matrix of PPCM with the embedded FN/FP's incorporated.
Tony Chiang
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,]