Simulate: S4 Generic method to Simulate SPR data

In ffeng23/SPRATS: An R package to do Two state modelling of SPR data

Description

Generic method to run the simulation based on the model

Usage

Simulate(x, sampleFreq = 0.01, sd = 0, fix.ligand = TRUE, ...)

## S4 method for signature 'LangmuirModel'
Simulate(x, sampleFreq = 0.01, sd = 0,
  fix.ligand = TRUE)

## S4 method for signature 'InducedFitModel'
Simulate(x, sampleFreq = 0.01, sd = 0,
  fix.ligand = TRUE)

## S4 method for signature 'ConformationalSelectionModel'
Simulate(x, sampleFreq = 0.01,
  sd = 0, fix.ligand = TRUE)

## S4 method for signature 'TwoStateModel'
Simulate(x, sampleFreq = 0.01, timeStep = 0.01,
  sd = 0, fix.ligand = TRUE)

Arguments

sampleFreq	numeric the time frequency to collect the SPR data
sd	standard deviation used to simulate the nosiy data. zero by default for non-noisy data
timeStep	numeric the time step used to run numerical simulation This is only for the Two State model, since the other 3 models are analytical calculated.
model	currently only used for two different model for Rmax: 1)model=1, fixed ligand immobilization model. Where Rmax is kept at a costant level for different run or different channel. only one Rmax is set through parameter "Rmax". 2)model=2,variable ligand immobilization model, where Rmax for each run/channel is not fixed and only "efficincy" is assumed to be constant. if model is set to be other values (not 1 or 2), fixed ligand model assumed.

Details

each model has different biochemical dynamics to generate the data. The Langmuir, induced fit and conformational selection models simulate data analytically, but the two state model simulates through numerical integration. Please check the details here http://

the output is the sensorgram data for AB, A and A_star warning though, the association data for A and A_star are good. The dissociation data for A is the sum of A and A_star since we can simply tell them apart with only R observed (R is the AB levels) So we simply add them together and save them in A@dissociationData and save nothing in A_star (no dissociation data). Note: this part is a bit confusing. Need more work in the future.

Value

a list of SensorgramData-class data object holding the SPR data for different component in the system

Methods (by class)

• LangmuirModel: to simulate the SPR data based on a Langmuir Model

• InducedFitModel: to simulate the SPR data based on a InducedFit Model

• ConformationalSelectionModel: to simulate the SPR data based on a ConformationalSelection Model

• TwoStateModel: to simulate the SPR data based on a TwoState Model

See Also

ConformatinalSelectionModel-class TwoStateModel-class InducedFitModel-class LangmuirModel-class SensorgramData-class

ffeng23/SPRATS documentation built on May 16, 2019, 12:50 p.m.