Entry: APComEX
Aliases: APComEX
Keywords: datasets
Description: An example of an ISI using apComplex on simEX
URL: ../../../library/simulatorAPMS/html/APComEX.html

Entry: PPIEX
Aliases: PPIEX
Keywords: datasets
Description: Protein-protein co-membership graph matrix
URL: ../../../library/simulatorAPMS/html/PPIEX.html

Entry: TSNMatrix
Aliases: TSNMatrix
Keywords: datasets
Description: ISI
URL: ../../../library/simulatorAPMS/html/TSNMatrix.html

Entry: applyDeformationError
Aliases: applyDeformationError
Keywords: datagen
Description: Function that handles deformed bait proteins
URL: ../../../library/simulatorAPMS/html/applyDeformationError.html

Entry: applyFNErrors
Aliases: applyFNErrors
Keywords: datagen
Description: Function that generates stochastic False Negative Errors
URL: ../../../library/simulatorAPMS/html/applyFNErrors.html

Entry: applyFPErrors
Aliases: applyFPErrors
Keywords: datagen
Description: Function to generate the False Postive Observations
URL: ../../../library/simulatorAPMS/html/applyFPErrors.html

Entry: applyStickyError
Aliases: applyStickyError
Keywords: datagen
Description: Function that takes sticky proteins and calculates FP's
URL: ../../../library/simulatorAPMS/html/applyStickyError.html

Entry: compIndep
Aliases: compIndep
Keywords: datagen
Description: This function determines probability distribution independence between two bi-partite graph incidence matrices.
URL: ../../../library/simulatorAPMS/html/compIndep.html

Entry: filteredProt
Aliases: filteredProt
Keywords: datasets
Description: A data file containing unusable proteins
URL: ../../../library/simulatorAPMS/html/filteredProt.html

Entry: fullSimEX
Aliases: fullSimEX
Keywords: datasets
Description: In Silico Interactome
URL: ../../../library/simulatorAPMS/html/fullSimEX.html

Entry: missedProtEX
Aliases: missedProtEX
Keywords: datasets
Description: Vector of Protein not recorded in simEX
URL: ../../../library/simulatorAPMS/html/missedProtEX.html

Entry: missedProtHMSPCI
Aliases: missedProtHMSPCI
Keywords: datasets
Description: The proteins not recorded by the ISI TSNMatrix
URL: ../../../library/simulatorAPMS/html/missedProtHMSPCI.html

Entry: recordSticky
Aliases: recordSticky
Keywords: datagen
Description: This function records proteins known to be sticky in the simulation of AP-MS.
URL: ../../../library/simulatorAPMS/html/recordSticky.html

Entry: runAPComplex
Aliases: runAPComplex
Keywords: datagen
Description: A function that calls the complex estimation function, apComplex on the simulated output from runSimulators
URL: ../../../library/simulatorAPMS/html/runAPComplex.html

Entry: runCompIndep
Aliases: runCompIndep
Keywords: datagen
Description: Function checks the arguments and parameters for compIndep.
URL: ../../../library/simulatorAPMS/html/runCompIndep.html

Entry: runSimEX
Aliases: runSimEX
Keywords: datasets
Description: The output of the simulation with fullSimEX as the input
URL: ../../../library/simulatorAPMS/html/runSimEX.html

Entry: runSimulators
Aliases: runSimulators
Keywords: misc
Description: Function that sets up the ISI et al to run the simulations
URL: ../../../library/simulatorAPMS/html/runSimulators.html

Entry: simEX
Aliases: simEX
Keywords: datasets
Description: An example ISI
URL: ../../../library/simulatorAPMS/html/simEX.html

Entry: simulator
Aliases: simulator
Keywords: misc
Description: Function sets up inputs to call all FN/FP errors on the PPCM
URL: ../../../library/simulatorAPMS/html/simulator.html

Entry: simulatorD
Aliases: simulatorD
Keywords: misc
Description: Function that simulates deformation errors
URL: ../../../library/simulatorAPMS/html/simulatorD.html

Entry: simulatorS
Aliases: simulatorS
Keywords: misc
Description: Function that calculates the FP sticky errors
URL: ../../../library/simulatorAPMS/html/simulatorS.html

Entry: vBaits
Aliases: vBaits
Keywords: datasets
Description: The baits used in HMSPCI
URL: ../../../library/simulatorAPMS/html/vBaits.html

Entry: vBaitsEX
Aliases: vBaitsEX
Keywords: datasets
Description: Example Vector of Baits
URL: ../../../library/simulatorAPMS/html/vBaitsEX.html

Entry: vDeformEX
Aliases: vDeformEX
Keywords: datasets
Description: Doformed Protein
URL: ../../../library/simulatorAPMS/html/vDeformEX.html

Entry: vDeformed
Aliases: vDeformed
Keywords: datasets
Description: A deformed protein
URL: ../../../library/simulatorAPMS/html/vDeformed.html

Entry: vDeformedEX
Aliases: vDeformedEX
Keywords: datasets
Description: Example vector of deformed baits
URL: ../../../library/simulatorAPMS/html/vDeformedEX.html

Entry: vStickyEX
Aliases: vStickyEX
Keywords: datasets
Description: Sticky Proteins
URL: ../../../library/simulatorAPMS/html/vStickyEX.html
