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BIGL (version 1.8.0)

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

558

Version

1.8.0

License

GPL-3

Issues

1

Pull Requests

0

Stars

7

Forks

8

Maintainer

Maxim Nazarov

Last Published

June 13th, 2023

Functions in BIGL (1.8.0)

contour.ResponseSurface

Method for plotting of contours based on maxR statistics
fitted.ResponseSurface

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

Partial data with combination experiments of direct-acting antivirals
generateData

Generate data from parameters of marginal monotherapy model
fitMarginals

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

Return a list with transformation functions
get.abs_tval

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

Estimate initial values for fitting marginal dose-response curves
plot.ResponseSurface

Method for plotting response surface objects
df.residual.MarginalFit

Residual degrees of freedom in marginal model estimation
plot.MarginalFit

Plot monotherapy curve estimates
isobologram

Isobologram of the response surface predicted by the null model
marginalOptim

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

Estimate CP matrix from bootstraps
getR

Helper functions for the test statistics
marginalNLS

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

Alternative Loewe generalization
modelVar

Calculate model variance, assuming variance increases linearly with mean
plot.meanR

Plot bootstrapped cumulative distribution function of meanR null distribution
meanR

Compute meanR statistic for the estimated model
maxR

Compute maxR statistic for each off-axis dose combination
optim.boxcox

Find optimal Box-Cox transformation parameters
predictResponseSurface

Predict the entire response surface, so including on-axis points, and return the result as a matrix. For plotting purposes.
getd1d2

A function to get the d1d2 identifier
hsa

Highest Single Agent model
plotMeanVarFit

Make a mean-variance plot
plotConfInt

Plot confidence intervals from BIGL object in a contour plot
predictVar

Predict variance
plot.effect-size

Plot of effect-size object
outsidePoints

List non-additive points
get.summ.data

Summarize data by factor
plot.maxR

Plot of maxR object
runBIGL

Run the BIGL application for demonstrating response surfaces
plotResponseSurface

Plot response surface
print.summary.MarginalFit

Print method for summary of MarginalFit object
print.summary.BIGLconfInt

Print summary of BIGLconfInt object
print.summary.meanR

Print summary of meanR object
residuals.MarginalFit

Residuals from marginal model estimation
vcov.MarginalFit

Estimate of coefficient variance-covariance matrix
summary.maxR

Summary of maxR object
print.summary.ResponseSurface

Print method for the summary function of ResponseSurface object
predict.MarginalFit

Predict values on the dose-response curve
summary.ResponseSurface

Summary of ResponseSurface object
sampleResids

Sample residuals according to a new model
simulateNull

Simulate data from a given null model and monotherapy coefficients
summary.meanR

Summary of meanR object
predictOffAxis

Compute off-axis predictions
plot.BIGLconfInt

Plot confidence intervals in a contour plot
scaleResids

Functions for scaling, and rescaling residuals. May lead to unstable behaviour in practice
synergy_plot_bycomp

Plot 2D cross section of response surface
print.summary.maxR

Print summary of maxR object
summary.BIGLconfInt

Summary of confidence intervals object
summary.MarginalFit

Summary of MarginalFit object
GetStartGuess

Estimate initial values for dose-response curve fit
bootConfInt

Obtain confidence intervals for the raw effect sizes on every off-axis point and overall
Blissindependence

Bliss Independence Model
boxcox.transformation

Apply two-parameter Box-Cox transformation
addResids

Add residuals by adding to mean effects
L4

4-parameter logistic dose-response function
constructFormula

Construct a model formula from parameter constraint matrix
col2hex

R color to RGB (red/green/blue) conversion.
coef.MarginalFit

Coefficients from marginal model estimation
backscaleResids

Backscale residuals
fitted.MarginalFit

Compute fitted values from monotherapy estimation
generalizedLoewe

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

Full data with combination experiments of direct-acting antivirals
fitSurface

Fit response surface model and compute meanR and maxR statistics