| smoke-package {smoke} | R Documentation |
Small Molecule Octet/BLI Kinetics Experiment
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:
| Package: | smoke |
| Type: | Package |
| Title: | Small Molecule Octet/BLI Kinetics Experiment |
| Version: | 2.0.1 |
| Date: | 2024-03-11 |
| Author: | Qingan Sun, Xiaojun Li, James C Sacchettini |
| Maintainer: | Qingan Sun <quinsun@gmail.com> |
| 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. |
| License: | GPL-2 | GPL-3 |
| Depends: | R (>= 3.5.0),methods,graphics, grDevices, stats, utils |
| Imports: | Rdpack |
| RdMacros: | Rdpack |
| LazyData: | true |
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 <quinsun@gmail.com>
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)