Package 'smoke'

Description

Bio-Layer Interferometry (BLI) is a technology to determine the binding kinetics between biomolecules. BLI signals are small and noisy when small molecules are investigated as ligands (analytes). We develop this package to process and analyze the BLI data acquired on Octet Red96 from Fortebio more accurately. Sun Q., Li X., et al (2020) <doi:10.1038/s41467-019-14238-3>. In this new version, we organize the BLI experiment data and analysis methods into a S4 class with self-explaining structure.

Details

The DESCRIPTION file:

Index of help topics:

Bli                     Constructor of "Bli" class
Bli-class               Class '"Bli"'
alignLoad               Align BLI traces with loading step
alignLoad-methods       ~~ Methods for Function 'alignLoad' ~~
baseline                Align BLI traces with baseline step
baseline-methods        ~~ Methods for Function 'baseline' ~~
bli                     BLI data example
doubleBlank             Substract the double-references
doubleBlank-methods     ~~ Methods for Function 'doubleBlank' ~~
estimate                Estimate initial kinetic parameters
estimate-methods        ~~ Methods for Function 'estimate' ~~
fitKinetics             Fit binding kinetics
fitKinetics-methods     ~~ Methods for Function 'fitKinetics' ~~
initialize-methods      ~~ Methods for Function 'initialize' ~~
kOff0                   Getter for "Bli" slot of 'kOff0'
kOff0-methods           ~~ Methods for Function 'kOff0' ~~
kOff0<-                 Setter for "Bli" slot of 'kOff0'
kOff0<--methods         ~~ Methods for Function 'kOff0<-' ~~
kOn0                    Getter for "Bli" slot of 'kOn0'
kOn0-methods            ~~ Methods for Function 'kOn0' ~~
kOn0<-                  Setter for "Bli" slot of 'kOn0'
kOn0<--methods          ~~ Methods for Function 'kOn0<-' ~~
kinetics                Output kinetics model
kinetics-methods        ~~ Methods for Function 'kinetics' ~~
ligand                  Getter for "Bli" slot of ligand concentration
ligand-methods          ~~ Methods for Function 'ligand' ~~
ligand<-                Setter for "Bli" slot of ligand concentration
ligand<--methods        ~~ Methods for Function 'ligand<-' ~~
nls-class               Class 'nls'
plotKinetics            Plot kinetics model fitting
plotKinetics-methods    ~~ Methods for Function 'plotKinetics' ~~
plotResiduals           Plot residuals from kinetics model fitting
plotResiduals-methods   ~~ Methods for Function 'plotResiduals' ~~
plotTraces              Plot BLI traces
plotTraces-methods      ~~ Methods for Function 'plotTraces' ~~
show-methods            ~~ Methods for Function 'show' ~~
smoke-package           Small Molecule Octet/BLI Kinetics Experiment
status                  Getter for data processing 'status'
status-methods          ~~ Methods for Function 'status' ~~
tExp                    Getter for BLI times 'tExp'
tExp-methods            ~~ Methods for Function 'tExp' ~~
tExp<-                  Setter for BLI times 'tExp'
tExp<--methods          ~~ Methods for Function 'tExp<-' ~~
traces                  Getter of BLI 'traces'
traces-methods          ~~ Methods for Function 'traces' ~~
traces<-                Setter of BLI 'traces'
traces<--methods        ~~ Methods for Function 'traces<-' ~~

'Smoke' is an object-based package to analyze kinetics data from BioLayer Interferometry (BLI). The example dataset was published in Nature Communication 2020, 11: 339.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)
bli5 <- fitKinetics(bli4)
plotTraces(bli2)
plotKinetics(bli5)
plotResiduals(bli5)

Description

Align BLI traces with loading step with the start and end times.

Usage

alignLoad(obj, loadStart, loadEnd)

Arguments

Details

This is the optional first step in BLI data processing. The traces in the input "Bli" object is assumed to be paired original dataset. The output "Bli" object contains the traces aligned, and the status of "alignLoad" set to "TRUE".

Value

S4 object of "Bli" class

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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

bli1 <- alignLoad(bli, 180, 780)

Description

~~ Methods for function alignLoad ~~

Methods

signature(obj = "Bli")

Description

Align BLI traces with the baseline step right before the association step. The start and end times of baseline are input arguments.

Usage

baseline(obj, tStart, tEnd)

Arguments

Details

This step follows doubleBlank step. The output "Bli" object contains the traces aligned with baselines, and the status of "baseline" set to "TRUE". Also the traces number will be checked. If it does not equal the number of ligand concentration, a warning will be raised: "ligand concentrations mis-match trace number".

Value

S4 object of "Bli" class

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)

Description

~~ Methods for function baseline ~~

Methods

signature(obj = "Bli")

Description

This is an unprocessed BLI data saved in a "BLI" object (Sun et al. 2020).

Usage

data("bli")

Format

A S4 "Bli" class with 7 slots.

status

a logical vector indicating this is a raw dataset

traces

a data.frame with 16 BLI traces at 12290 time points

ligand

a numeric vector of ligand concentrations

tExp

a numeric vector of association and dissociation times

kOn0

a numeric of initial on-rate; empty

kOff0

a numeric of initial off-rate; empty

kinetics

a nls object; empty

Source

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

data(bli)

Description

Construction of a new "Bli" object with all slots initialized.

Usage

Bli(...)

Arguments

Value

S4 object of "Bli" class

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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).

See Also

Bli-class

Examples

bli1 <- Bli()

Description

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

Arguments

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 <[email protected]>

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")

Description

The BLI experiment for small-molecules is designed to have double references: reference biosensor and reference sample, i.e. b

Usage

doubleBlank(obj)

Arguments

Details

The signal in small-molecule BLI experiment is small in relation to noise. So the experiment design includes double references: reference biosensor and reference sample (no ligand). With subtraction of both, we expect to remove both the background signal and the non-specific binding.
The doubleBlank assumes that traces in the input "Bli" object contains two consecutive sets of columns with the second set as the refence biosensor, and the reference samples as the last column in each set. This means that the traces are "paired" and traces number is even. If not, an error message will be raised: "the double-referenced traces should be paired".
After doubleBlank, the number of traces should be equal to the number of ligand concentration. If not, a warning will be raised: "ligand concentrations mis-match trace number".
Also, after successful doubleBlank, the status of "doubleBlank" will be set to "TRUE". This prevent the user to run doubleBlank twice in accident.

Value

S4 object of "Bli" class

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)

Description

~~ Methods for function doubleBlank ~~

Methods

signature(obj = "Bli")

Description

Estimate the initial kinetic parameters, kOn0 and kOff0, and save in the returned "Bli" object. These parameters can serve as the starting value in the next step, fitKinetics, to calculate the kinetics binding model of the small-molecule under investigation.

Usage

estimate(obj)

Arguments

Value

S4 object of "Bli" class

Note

kOn0 and kOff0 can also be input manually with the setter functions, kOn0<- and kOff0<-.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)

Description

~~ Methods for function estimate ~~

Methods

signature(obj = "Bli")

Description

Fit the BLI traces with a single association-then-dissociation equation.

Usage

fitKinetics(obj)

Arguments

Details

We fit the whole set of BLI traces with a single association-then-dissociation equation (Sun et al. 2020). The fitting model will be stored in the kinetics slot, and the status of "fitKinetics" will be set to "TRUE".

Value

S4 object of "Bli" class

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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).

See Also

kinetics, plotKinetics, plotResiduals

Examples

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)
bli5 <- fitKinetics(bli4)

Description

~~ Methods for function fitKinetics ~~

Methods

signature(obj = "Bli")

Description

~~ Methods for function initialize ~~

Methods

signature(.Object = "Bli")

Description

Output kinetics model with matrix containing KD, rMax, kOn, kOff, and the relevant statistics.

Usage

kinetics(obj)

Arguments

Value

"matrix" with kinetic parameters

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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).

See Also

fitKinetics

Examples

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)
bli5 <- fitKinetics(bli4)
kinetics(bli5)

Description

~~ Methods for function kinetics ~~

Methods

signature(obj = "Bli")

Description

The getter function for "Bli" slot of kOff0, initial kOff rate.

Usage

kOff0(obj)

Arguments

Value

numeric of kOff0

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

estimate

Examples

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)
kOff0(bli4)

Description

~~ Methods for function kOff0 ~~

Methods

signature(obj = "Bli")

Description

The setter function for "Bli" slot of kOff0, initial kOff rate

Usage

kOff0(obj) <- value

Arguments

Value

S4 object of "Bli" class

Note

It is preferred to estimate initial kOff rate.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

estimate

Examples

bli <- Bli()
kOff0(bli) <- 0.1

Description

~~ Methods for function kOff0<- ~~

Methods

signature(obj = "Bli")

Description

The getter function for "Bli" slot of kOn0, initial kOn rate.

Usage

kOn0(obj)

Arguments

Value

numeric of kOn0

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

estimate

Examples

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)
kOn0(bli4)

Description

~~ Methods for function kOn0 ~~

Methods

signature(obj = "Bli")

Description

The setter function for "Bli" slot of kOn0, initial kOn rate.

Usage

kOn0(obj) <- value

Arguments

Value

S4 object of "Bli" class

Note

It is preferred to estimate initial kOn rate.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

estimate

Examples

bli <- Bli()
kOn0(bli) <- 0.1

Description

~~ Methods for function kOn0<- ~~

Methods

signature(obj = "Bli")

Description

The getter function for "Bli" slot of ligand concentration. If the slot is empty, there will be an error message: "please input ligand concentration".

Usage

ligand(obj)

Arguments

Value

a numeric vector for the ligand concentration in BLI experiment

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

ligand<-

Examples

conc <- ligand(bli)

Description

~~ Methods for function ligand ~~

Methods

signature(obj = "Bli")

Description

The setter function for "Bli" slot of ligand concentration in BLI experiment.

Usage

ligand(obj) <- value

Arguments

Value

S4 object of "Bli" class

Note

The ligand concentrations do not include the blank control (0).

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

ligand

Examples

bli1 <- Bli()
ligand(bli1) <- 16/2^(0:6)

Description

~~ Methods for function ligand<- ~~

Methods

signature(obj = "Bli")

Description

Registration of S3 nls into S4 class.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

Description

Plot the BLI traces with the kinetics-model fitting.

Usage

plotKinetics(obj, ...)

Arguments

Note

This method only works after fitKinetics.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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).

See Also

fitKinetics, plotResiduals

Examples

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)
bli5 <- fitKinetics(bli4)
plotKinetics(bli5)

Description

~~ Methods for function plotKinetics ~~

Methods

signature(obj = "Bli")

Description

Plot the residuals from the kinetics-model fitting

Usage

plotResiduals(obj, ...)

Arguments

Note

This method only works after fitKinetics.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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).

See Also

fitKinetics, plotKinetics

Examples

bli1 <- alignLoad(bli, 180, 780)
bli2 <- doubleBlank(bli1)
bli3 <- baseline(bli2, 1080, 1260)
bli4 <- estimate(bli3)
bli5 <- fitKinetics(bli4)
plotResiduals(bli5)

Description

~~ Methods for function plotResiduals ~~

Methods

signature(obj = "Bli")

Description

Plot the BLI traces in the "Bli" object.

Usage

plotTraces(obj, ...)

Arguments

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

plotKinetics, plotResiduals

Examples

plotTraces(bli)

Description

~~ Methods for function plotTraces ~~

Methods

signature(obj = "Bli")

Description

~~ Methods for function show ~~

Methods

signature(object = "Bli")

Description

The getter function for the data processing status.

Usage

status(obj)

Arguments

Value

"logical" vector as the indicator of the status of data analysis

Note

There is no Setter for status by design.
Because status is modified automatically during data processing, there is no need for the user to change the status manually.

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

See Also

alignLoad, doubleBlank, baseline, estimate, fitKinetics

Examples

bli <- Bli()
status(bli)

Description

~~ Methods for function status ~~

Methods

signature(obj = "Bli")

Description

The getter function for BLI times tExp, the start time of association and dissociation steps.

Usage

tExp(obj)

Arguments

Value

"numeric" vector for the start time of association and dissociation steps

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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

tExp(bli)

Description

~~ Methods for function tExp ~~

Methods

signature(obj = "Bli")

Description

The setter function for BLI times tExp, the start time of association and dissociation steps.

Usage

tExp(obj) <- value

Arguments

Value

S4 object of "Bli" class

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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

bli <- Bli()
tExp(bli) <- c(1260,1860)

Description

~~ Methods for function tExp<- ~~

Methods

signature(obj = "Bli")

Description

The getter function of BLI traces. The first column of this data.frame is the time in second; the following columns are the BLI traces.

Usage

traces(obj)

Arguments

Value

"data.frame" of BLI traces

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

Examples

traces(bli)

Description

~~ Methods for function traces ~~

Methods

signature(obj = "Bli")

Description

The setter function of BLI traces. The input "data.frame" contains the times in the first column and the BLI traces in the following columns.

Usage

traces(obj) <- value

Arguments

Details

There may be two kinds of input "data.frame":
The "original" data with times in the first column, and two consecutive sets of BLI traces in the remaining columns. The second set are the traces from the reference biosensor. In both sets, the last trace is from the reference sample (no ligand).
The user may input the traces of which the double references have been subtracted. In this case, the first column is still the time. The rest of the columns contain the traces with the exact number of the length of ligand concentration.

Value

S4 object of "Bli" class

Author(s)

Qingan Sun, Xiaojun Li, James C Sacchettini

Maintainer: Qingan Sun <[email protected]>

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).

See Also

doubleBlank

Examples

bli <- Bli()
# traces(bli) <- read.csv("traces.csv")

Description

~~ Methods for function traces<- ~~

Methods

signature(obj = "Bli")