summary-der {chipPCR} | R Documentation |
Summary der
objects
Description
Summarize der
objects and easily access results of
inder
function.
Usage
## S4 method for signature 'der'
summary(object, digits = getOption("digits") - 3, print = TRUE)
Arguments
object |
is a |
digits |
is a |
print |
is a |
Details
The approximate second derivative maximum (SDM) which is commonly used to quantify quantitative real-time PCR experiments. The SDM might also be useful for isothermal amplification processes. The SDM is calculated from a derived cubic spline. Similarly the first approximate approximate derivative maximum (FDM), second derivative minimum (SDm), and approximate second derivative center (SDC, geometric mean of SDM and SDm) are available. FDM, SDm and SDC values can be used to further characterize the amplification process.
Value
A named vector of four elements. The element named 2nd_der
contains
values of the second first derivative. The element named SDM
contains approximate second derivative maximum, SDm
contains
approximate second derivative minimum, and SDC
contains approximate
second derivative center.
Author(s)
Stefan Roediger, Michal Burdukiewicz
References
Ruijter JM, Pfaffl MW, Zhao S, et al. (2013) Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications. Methods San Diego Calif 59:32–46.
See Also
Examples
res <- AmpSim(cyc = 1:40, Cq = 25)
test.der <- inder(res)
#just print summary
summary(test.der)
#print without rounding
summary(test.der, digits = 6)
#assign summary to variable without printing and
vals <- summary(test.der, print = FALSE)
print(vals)
#easily access different values
vals["bg.start"]