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 |