Bli-class {smoke}

Class "Bli"

Description

Bli is a S4 class to contain the Bli experiment data and analysis result.

Arguments

...

.Object in initialize; leave empty

Objects from the Class

Objects can be created by calls of the form Bli(...).

Slots

traces:

Object of class "data.frame" of BLI traces; "time" in the 1st column

lig:

Object of class "numeric" of ligand concentrations

tExp:

Object of class "numeric" of association and dissociation times

status:

Object of class "vector" indicator and record of processing

kinetics:

Object of class "nls" model of binding kinetics

kOn0:

Object of class "numeric" initial value of on-rate

kOff0:

Object of class "numeric" initial value of off-rate

Methods

alignLoad

signature(obj = "Bli"): Align BLI traces with loading step

baseline

signature(obj = "Bli"): Align BLI traces with baseline step

doubleBlank

signature(obj = "Bli"): Substract the double-references

estimate

signature(obj = "Bli"): Estimate initial kinetic parameters

fitKinetics

signature(obj = "Bli"): Fit binding kinetics

initialize

signature(.Object = "Bli"): initializer

kinetics

signature(obj = "Bli"): Output kinetics model

kOff0

signature(obj = "Bli"): Getter for "Bli" slot of kOff0

kOff0<-

signature(obj = "Bli"): Setter for "Bli" slot of kOff0

kOn0

signature(obj = "Bli"): Getter for "Bli" slot of kOn0

kOn0<-

signature(obj = "Bli"): Setter for "Bli" slot of kOn0

ligand

signature(obj = "Bli"): Getter for ligand concentration

ligand<-

signature(obj = "Bli"): Setter for ligand concentration

plotKinetics

signature(obj = "Bli"): Plot kinetics model fitting

plotResiduals

signature(obj = "Bli"): Plot residuals from kinetics model fitting

plotTraces

signature(obj = "Bli"): Plot BLI traces

show

signature(object = "Bli"): show method

status

signature(obj = "Bli"): Getter for data processing status

tExp

signature(obj = "Bli"): Getter for BLI times tExp

tExp<-

signature(obj = "Bli"): Setter for BLI times tExp

traces

signature(obj = "Bli"): Getter of BLI traces

traces<-

signature(obj = "Bli"): Setter of BLI traces

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[e-mail]>

References

Sun Q, Li X, Perez LM, Shi W, Zhang Y, Sacchettini JC (2020). “The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD.” Nature Communications, 11(339).

Examples

showClass("Bli")