Computationally simulates the AP-MS technology.


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Documentation for package `simulatorAPMS' version 1.8.0

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APComEX An example of an ISI using apComplex on simEX
applyDeformationError Function that handles deformed bait proteins
applyFNErrors Function that generates stochastic False Negative Errors
applyFPErrors Function to generate the False Postive Observations
applyStickyError Function that takes sticky proteins and calculates FP's
compIndep This function determines probability distribution independence between two bi-partite graph incidence matrices.
filteredProt A data file containing unusable proteins
fullSimEX In Silico Interactome
missedProtEX Vector of Protein not recorded in simEX
missedProtHMSPCI The proteins not recorded by the ISI TSNMatrix
PPIEX Protein-protein co-membership graph matrix
recordSticky This function records proteins known to be sticky in the simulation of AP-MS.
runAPComplex A function that calls the complex estimation function, apComplex on the simulated output from runSimulators
runCompIndep Function checks the arguments and parameters for compIndep.
runSimEX The output of the simulation with fullSimEX as the input
runSimulators Function that sets up the ISI et al to run the simulations
simEX An example ISI
simulator Function sets up inputs to call all FN/FP errors on the PPCM
simulatorD Function that simulates deformation errors
simulatorS Function that calculates the FP sticky errors
TSNMatrix ISI
vBaits The baits used in HMSPCI
vBaitsEX Example Vector of Baits
vDeformed A deformed protein
vDeformedEX Example vector of deformed baits
vDeformEX Doformed Protein
vStickyEX Sticky Proteins