fitMusycModel {braidrm} | R Documentation |
MuSyC Response Surface Fitting
Description
Fits the Multidimensional Synergy of Combinations (MuSyC) model of combined action to the given data (Wooten et al. 2021).
Usage
fitMusycModel(
formula,
data,
variant = "standard",
weights = NULL,
direction = 0,
lower = NULL,
upper = NULL
)
## S3 method for class 'formula'
fitMusycModel(
formula,
data,
variant = "standard",
weights = NULL,
direction = 0,
lower = NULL,
upper = NULL
)
## Default S3 method:
fitMusycModel(
formula,
data,
variant = "standard",
weights = NULL,
direction = 0,
lower = NULL,
upper = NULL
)
Arguments
formula |
Either an object of class |
data |
If |
variant |
String specifying which variant of the MuSyC model is to be
fit to the data. If "standard" (the default), all MuSyC parameters except
|
weights |
An optional vector of weights the same length as |
direction |
Determines the possible directionality of the BRAID model. If 0 (the default) no additional constraints are placed on the parameters. If greater than 0, the fitting will require that the maximal effects are all greater than or equal to the minimal effect. If less than 0, the fitting will require that all maximal effect is less than or equal to the minimal effect. |
lower |
An optional set of lower bounds on the fitted MuSyC response parameters. Any values set to NA will be filled with default calculated bounds. May be length 4 (will be treated as a set of lower bounds on the minimal and maximal effect parameters only), length 8 (will be treated as lower bounds on the four individual dose response parameters and the four minimal and maximla effect parameters), the same length as the space of parameters being optimized (8 for "independent", 10 for "standard", or 12 for "full"), or length 12. |
upper |
An optional set of lower bounds on the fitted MuSyC response
parameters. Behaves the same as |
Value
An object of class braidAltFit
with the following values:
-
concs
: The array of concentrations passed to the functions -
act
: The vector of measurements associated with the given dose pairs -
weights
: The vector of weights for the given measurements, set to 1 for all measurements by default -
method
: Specifying the alternate surface model being used (in this case "MuSyC") -
variant
: A string specifying which MuSyC variant was fit: "independent", "standard", or "full" -
coefficients
: A parameter vector of the appropriate length forvariant
specifying the best fit response surface -
fitted.values
: The predicted response surface value for the given dose pairs and best-fit response surface -
residuals
: The difference between the predicted and measured values for the given dose pairs, always equal to "measured minus predicted" -
direction
: The direction value passed to the function -
pbounds
': A 2-by-k array of bounds on the MuSyC parameters used in the parameter optimization
References
Wooten, David J, Christian T Meyer, Alexander LR Lubbock, Vito Quaranta, and Carlos F Lopez. 2021. “MuSyC Is a Consensus Framework That Unifies Multi-Drug Synergy Metrics for Combinatorial Drug Discovery.” Nature Communications 12 (1): 4607.
Examples
mfit1 <- fitMusycModel(measure ~ concA + concB, synergisticExample)
coef(mfit1)
mfit2 <- fitMusycModel(measure ~ concA + concB, oppositionalExample,
variant = "independent")
coef(mfit2)