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

Entry: JaccardCoef
Aliases: JaccardCoef
Keywords: misc
Description: Function to calculate the Jaccard Coefficient
URL: ../../../library/simulatorAPMS/html/JaccardCoef.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: misc
Description: Function to calculate the Deformation Errors of AP-MS
URL: ../../../library/simulatorAPMS/html/applyDeformationError.html

Entry: applyFNErrors
Aliases: applyFNErrors
Keywords: misc
Description: Function to calculate FN Errors in AP-MS
URL: ../../../library/simulatorAPMS/html/applyFNErrors.html

Entry: applyFPErrors
Aliases: applyFPErrors
Keywords: misc
Description: Function to calculate FP Errors in AP-MS
URL: ../../../library/simulatorAPMS/html/applyFPErrors.html

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

Entry: compBijection
Aliases: compBijection
Keywords: misc
Description: Function that calculates an alignment between ISI and estimate based on some similarity measure, e.g Jaccard
URL: ../../../library/simulatorAPMS/html/compBijection.html

Entry: compIndep
Aliases: compIndep
Keywords: misc
Description: This function determines how independent the prob distribution of the TSN and the estimate are with respect to one another
URL: ../../../library/simulatorAPMS/html/compIndep.html

Entry: compareComplex
Aliases: compareComplex
Keywords: misc
Description: Function to compare the ISI to the estimate
URL: ../../../library/simulatorAPMS/html/compareComplex.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 (the example ISI)
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: misc
Description: This function records the sticky proteins in the simulation of AP-MS
URL: ../../../library/simulatorAPMS/html/recordSticky.html

Entry: runAPComplex
Aliases: runAPComplex
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/simulatorAPMS/html/runAPComplex.html

Entry: runAlignment
Aliases: runAlignment
Keywords: misc
Description: Function preparing for alignment
URL: ../../../library/simulatorAPMS/html/runAlignment.html

Entry: runCompIndep
Aliases: runCompIndep
Keywords: misc
Description: Function that sets up prelims for compIndep.R
URL: ../../../library/simulatorAPMS/html/runCompIndep.html

Entry: runCompareComplex
Aliases: runCompareComplex
Keywords: misc
Description: Function that sets up the ISI and estimate matrix for compare complex
URL: ../../../library/simulatorAPMS/html/runCompareComplex.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
