fitModelNlmeData: Fit an nlme dose reponse model to GDSC data.

In CancerRxGene/gdscIC50: Pipeline for GDSC Curve Fitting

Fit an nlme dose reponse model to GDSC data.

Description

Fit an nlme dose reponse model to GDSC data.

Usage

fitModelNlmeData(nlme_data, isLargeData = T)

Arguments

nlme_data

a data frame as specified by prepNlmeData

isLargeData

logical. Default (isLargeData = T). Set to F if model fitting fails to converge, e.g., step halving factor reduced below minimum in PNLS step With this isLargeData = TRUE, the covariance between the position and scale parameter on the cell line level are assumed to be correlated. This further stabilizes the fit. In small bespoke screens this is set to FALSE as the model otherwise struggles to converge.

Value

a fitted nlme model

See Also

prepNlmeData, getModelCoef, calcNlmeStats.

Examples

data("gdsc_example")
gdsc_example <- removeFailedDrugs(gdsc_example)
gdsc_example <- removeMissingDrugs(gdsc_example)
gdsc_example <- normalizeData(gdsc_example)
gdsc_example <- setConcsForNlme(gdsc_example)
nlme_data <- prepNlmeData(gdsc_example, "COSMIC_ID")
## Not run: 
nlme_model <- fitModelNlmeData(nlme_data, isLargeData = F)

## End(Not run)

CancerRxGene/gdscIC50 documentation built on Oct. 6, 2022, 2:40 a.m.