simulatorS {simulatorAPMS}R Documentation

Function that calculates the FP sticky errors

Description

The simulatorS function is the function that operates on sticky baits. It takes in a vector of sticky baits, and for each bait B, it finds all the proteins not interacting with it in the ISI. When it has calculated this set of proteins, it calls the applyStickyErrors function and gets the subset of proteins as the FP hits. It changes these interactions from 0 to 1 in the PPCM matrix creating an directed graph PPCM matrix with error.

Usage

simulatorS(stickyBaits, rateS, TSNMat, exMat)

Arguments

stickyBaits A vector of baits known to be sticky
rateS A single rate of a vector of rates which the experiment will record FP's due to the sticky proteins
TSNMat The ISI matrix
exMat The experimental matrix that carries the FP/FN

Details

One interesting aspect of this function is that the rateS can either be a vector of the same length as the vector of sticky baits, or it can be a single rate which is applied to all the sticky baits. The function calls applyStickyErrors on the prescribed sticky baits to assign FP observations onto them. This FP rate is different than the general rateFP and is determined by rateS

Value

The return value of this function is the adjusted PPCM matrix with error to reflect the FP's that have been induced by applyStickyErrors

Author(s)

Tony Chiang

See Also

simulatorS

Examples


library(apComplex)
data(MBMEcHMSPCI)
data(HMSPCI)
vBaits = rownames(HMSPCI)[1:10]
PPI = MBMEcHMSPCI 
mode(PPI) = "logical"
mode(PPI) = "numeric"
exMat = PPI[vBaits,]
stickyBaits = vBaits[2:3]
rateS = 0.9
test = simulatorS(stickyBaits, rateS, MBMEcHMSPCI, exMat) 
test[2:3,]


[Package simulatorAPMS version 1.2.1 Index]