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BIGL (version 1.5.3)

Biochemically Intuitive Generalized Loewe Model

Description

Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) .

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Install

install.packages('BIGL')

Monthly Downloads

545

Version

1.5.3

License

GPL-3

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Repository

https://github.com/openanalytics/BIGL

Maintainer

Maxim Nazarov

Last Published

September 10th, 2020

Functions in BIGL (1.5.3)

coef.MarginalFit

Coefficients from marginal model estimation

4-parameter logistic dose-response function

Data generating function used for constructing null distribution of meanR and maxR statistics

df.residual.MarginalFit

Residual degrees of freedom in marginal model estimation

Estimate initial values for dose-response curve fit

Blissindependence

Bliss Independence Model

contour.ResponseSurface

Method for plotting of contours based on maxR statistics

Estimate CP matrix with bootstrap

boxcox.transformation

Apply two-parameter Box-Cox transformation

constructFormula

Construct a model formula from parameter constraint matrix

Return absolute t-value, used in optimization call in optim.boxcox

Fit two 4-parameter log-logistic functions for a synergy experiment

Summarize data by factor

directAntivirals_ALL

Full data with combination experiments of direct-acting antivirals

directAntivirals

Partial data with combination experiments of direct-acting antivirals

Compute maxR statistic for each off-axis dose combination

Fit two 4-parameter log-logistic functions with common baseline

initialMarginal

Estimate initial values for fitting marginal dose-response curves

Highest Single Agent model

Fit response surface model and compute meanR and maxR statistics

getTransformations

Return a list with transformation functions

Alternative Loewe generalization

plotResponseSurface

Plot response surface

Simulate data from a given null model and monotherapy coefficients

Plot bootstrapped cumulative distribution function of meanR null distribution

plot.ResponseSurface

Method for plotting response surface objects

Plot of maxR object

Summary of meanR object

vcov.MarginalFit

Estimate of coefficient variance-covariance matrix

summary.MarginalFit

Summary of MarginalFit object

Summary of maxR object

summary.ResponseSurface

Summary of ResponseSurface object

Generate data from parameters of marginal monotherapy model

generalizedLoewe

Compute combined predicted response from drug doses according to standard or generalized Loewe model.

predict.MarginalFit

Predict values on the dose-response curve

Run the BIGL application for demonstrating response surfaces

Compute off-axis predictions

residuals.MarginalFit

Residuals from marginal model estimation

fitted.ResponseSurface

Predicted values of the response surface according to the given null model

fitted.MarginalFit

Compute fitted values from monotherapy estimation

plot.MarginalFit

Plot monotherapy curve estimates

List non-additive points

Isobologram of the response surface predicted by the null model

Fit two 4-parameter log-logistic functions with non-linear least squares

Compute meanR statistic for the estimated model

Find optimal Box-Cox transformation parameters

print.summary.ResponseSurface

Print method for the summary function of ResponseSurface object

print.summary.MarginalFit

Print method for summary of MarginalFit object

print.summary.meanR

Print summary of meanR object

print.summary.maxR

Print summary of maxR object