runAPComplex {simulatorAPMS}R Documentation

~~function to do ... ~~

Description

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.

Usage

runAPComplex(errorModel, vBaits)

Arguments

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

Details

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.

Value

The return value errorComplex is the Bipartite Graph Matrix estimated by apComplex

Author(s)

Tony Chiang


[Package simulatorAPMS version 1.2.1 Index]