APComEX                 An example of an ISI using apComplex on simEX
JaccardCoef             Function to calculate the Jaccard Coefficient
PPIEX                   Protein-protein co-membership graph matrix
TSNMatrix               ISI
applyDeformationError   Function to calculate the Deformation Errors of
                        AP-MS
applyFNErrors           Function to calculate FN Errors in AP-MS
applyFPErrors           Function to calculate FP Errors in AP-MS
applyStickyError        Function that takes sticky proteins and
                        calculates FP's
compBijection           Function that calculates an alignment between
                        ISI and estimate based on some similarity
                        measure, e.g Jaccard
compIndep               This function determines how independent the
                        prob distribution of the TSN and the estimate
                        are with respect to one another
compareComplex          Function to compare the ISI to the estimate
fullSimEX               In Silico Interactome
missedProtEX            Vector of Protein not recorded in simEX (the
                        example ISI)
missedProtHMSPCI        The proteins not recorded by the ISI TSNMatrix
recordSticky            This function records the sticky proteins in
                        the simulation of AP-MS
runAPComplex            ~~function to do ... ~~
runAlignment            Function preparing for alignment
runCompIndep            Function that sets up prelims for compIndep.R
runCompareComplex       Function that sets up the ISI and estimate
                        matrix for compare complex
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
vBaits                  The baits used in HMSPCI
vBaitsEX                Example Vector of Baits
vDeformEX               Doformed Protein
vDeformed               A deformed protein
vDeformedEX             Example vector of deformed baits
vStickyEX               Sticky Proteins
