summary.refMFI

summary,refMFI-method

object


is a <code>numeric</code> value determining the number of decimal places. Used 
only
for printed values. See <a rd-options="base" href="/link/format?package=chipPCR&version=0.0.8-10&to=base" data-mini-rdoc="base::format">format</a>.


digits


is a <code>logical</code> value determining if pretty summary of the object 
should be printed.


print


Summarize <code>refMFI</code> objects and access general statistics 
of amplification reaction. refMFI means referenced Mean Fluorescence 
Intensity (Roediger et al. 2013).


manip

summary-refMFI

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.

summary-refMFI: Summary `refMFI` objects

Description

Usage

Arguments

References

See Also

Examples