runAPComplex {simulatorAPMS} | R Documentation |
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.
runAPComplex(errorModel, vBaits)
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 |
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.
The return value errorComplex is the Bi-partite Graph Incidence Matrix estimated by apComplex.
Tony Chiang
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)