qpcr_nlme: 5-parameter logistic mixed model analysis of qpcr data

In daniel-gerhard/qpcrnlme: Nonlinear mixed model analysis of RT-PCR data

Description

Fits a nonlinear mixed model to qpcr fluorescence data, allowing for one factorial ANOVA designs with several levels for a single treatment factor at multiple genes. Marginal c(t) values are calculated.

Usage

qpcr_nlme(response, cycle, gene, treatment, brep, well, data, 
 cutoff, nGQ=5, verbose=TRUE)

Arguments

response	Name of a column in data, denoting a numeric response vector with fluorescence observations.
cycle	Name of a column in data, denoting a numeric response vector with cycle numbers.
gene	Name of a column in data, denoting a factor coding for different genes.
treatment	Name of a column in data, denoting a factor coding for several treatment groups
brep	Name of a column in data, denoting a factor coding for biological replications.
well	Name of a column in data, denoting a factor coding for technical replications.
data	A data.frame object.
cutoff	cutoff value t to define c(t) cycle thresholds.
nGQ	Number of nodes and weights for Gaussian Quadrature
verbose	Some text output during calculation...

Value

An object of class ddct.

Author(s)

Daniel Gerhard <[e-mail]>

See Also

nlme

Examples

## Not run: 
data(pt6c)
pt6c$Time <- as.factor(pt6c$Time)
pt6result <- qpcr_nlme(response="Fluorescence", cycle="Cycle", gene="Target", 
                       treatment="Time", brep="Content", well="Well", 
                       data=pt6c, cutoff=100, verbose=TRUE)

data(pt3c)
pt3c$Time <- as.factor(pt3c$Time)
pt3result <- qpcr_nlme(response="Fluorescence", cycle="Cycle", gene="Target", 
                       treatment="Time", brep="Content", well="Well", 
                       data=pt3c, cutoff=100, verbose=TRUE)

data(KOTWTcurves)
Kresult <- qpcr_nlme(response="Fluorescence", cycle="Cycle", gene="Target", treatment="Sample", brep="Content", well="Well", 
                     data=KOTWTcurves, cutoff=100, verbose=TRUE)

data(QTTWTcurves)
Qresult <- qpcr_nlme(response="Fluorescence", cycle="Cycle", gene="Target", treatment="Sample", brep="Content", well="Well", 
                     data=QTTWTcurves, cutoff=10, nGQ=5, verbose=TRUE)
                     

## End(Not run)

daniel-gerhard/qpcrnlme documentation built on May 14, 2019, 3:39 p.m.