runAPComplex {simulatorAPMS}R Documentation

A function that calls the complex estimation function, apComplex on the simulated output from runSimulators

Description

The runAPComplex function takes the simulated AP-MS experimental data (represented as an adjacency matrix) and deletes the proteins from this matrix that is either not used as a bait nor ever seen as a prey in the experiment. After the deletion, the apComplex is called on the resulting matrix.

Usage

runAPComplex(errorModel, vBaits)

Arguments

errorModel An adjacency matrix: the rows are indexed by the baits and the columns are indexed by all the proteins found in the organism or cell under certain conditions
vBaits A character vector: baits used in the simulated AP-MS experiment

Details

This function runs the estimation algorithm apComplex. The algorithm accomplishes two things: it makes decision on if a directed edge is a True Positive (TP) or False Positive (FP) and if a missing directed edge is a True Negative (TN) or False Negative; after total reciprocity is decided, apComplex estimates the protein complex bi-partite graph matrix.

Value

The return value errorComplex is the Bi-partite Graph Incidence Matrix estimated by apComplex.

Author(s)

Tony Chiang

Examples

library(simulatorAPMS)
data(TSNMatrix)
data(vBaits)
data(missedProtEX)
sim = runSimulators(TSNMatrix, vBaits, vBaits[2], vBaits[5], 0.0003,
0.1, 0, 0, missedProtEX, 357)
runAPComplex(sim, vBaits)

[Package simulatorAPMS version 1.8.0 Index]