Computationally simulates the AP-MS technology.

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Documentation for package `simulatorAPMS' version 1.2.1

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APComEX An example of an ISI using apComplex on simEX
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
compareComplex Function to compare the ISI to the estimate
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
fullSimEX In Silico Interactome
JaccardCoef Function to calculate the Jaccard Coefficient
missedProtEX Vector of Protein not recorded in simEX (the example ISI)
missedProtHMSPCI The proteins not recorded by the ISI TSNMatrix
PPIEX Protein-protein co-membership graph matrix
recordSticky This function records the sticky proteins in the simulation of AP-MS
runAlignment Function preparing for alignment
runAPComplex ~~function to do ... ~~
runCompareComplex Function that sets up the ISI and estimate matrix for compare complex
runCompIndep Function that sets up prelims for compIndep.R
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