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 |