runAPComplex {simulatorAPMS} | R Documentation |
The runAPComplex function takes the simulated AP-MS experiment and deletes the proteins from the PPI 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 new PPCM matrix.
runAPComplex(errorModel, vBaits)
errorModel |
The simulated PPCM matrix where 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 |
The vector of 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 TP or FP and if a missing directed edge is a TN or FN; after total reciprocity is decided, apComplex estimates the protein complex interactome.
The return value errorComplex is the Bipartite Graph Matrix estimated by apComplex
Tony Chiang