chipPCR (version 1.0-2)

summary-der: Summary der objects

Description

Summarize '>der objects and easily access results of inder function.

Usage

# S4 method for der
summary(object, digits = getOption("digits") - 3, print = TRUE)

Arguments

object

is a '>der object.

digits

is a numeric value determining the number of decimal places. Used only for printed values. See format.

print

is a logical value determining if pretty summary of the object should be printed.

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.

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.

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

'>der

Examples

# NOT RUN {
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"]
# }