plot.eff

plot,eff-method

plot,eff,ANY-method

is a <code><a href="/link/?package=chipPCR&version=1.0-2" eff'="" data-mini-rdoc="chipPCR::"></a>'>eff</code> object.

xlab

ylab

main

Setting the option <code>trend = TRUE</code> shows the linear 
 regression line in the plot.

trend

If <code>res.fit</code> sets where the results (goodness of fit, amplification 
 efficiency, correlation ) of the linear regression line in the plot should be plotted.
 Accepts the same location keywords as <code><a rd-options="graphics" href="/link/legend?package=chipPCR&version=1.0-2&to=graphics" data-mini-rdoc="graphics::legend">legend</a></code>

res.fit

Setting the option <code>CI = TRUE</code> shows the confidence
 interval lines in the plot.

level

is a graphical parameter setting the plot use lines, points 
 or both (see <code><a rd-options="" href="/link/plot?package=chipPCR&version=1.0-2" data-mini-rdoc="chipPCR::plot">plot</a></code>).

type

is a graphical parameter used to define the symbol used in 
 the plot.

<code>length</code> is a graphical parameter used to define the 
 length of the error bar used in the plot.

er.length

<code>col</code> is a graphical parameter used to define the color of the points
 on the plot.

Draws diagnostic plots of the amplification efficiency.

hplot

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. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

Stefan Roediger

chipPCR

Toolkit of Helper Functions to Pre-Process Amplification Data

Michal Burdukiewicz

Konstantin A. Blagodatskikh

Andrej-Nikolai Spiess

plot.eff function

is a <code><a href='<a href='eff'></a>'>eff</a></code> object.

If <code>res.fit</code> sets where the results (goodness of fit, amplification 
 efficiency, correlation ) of the linear regression line in the plot should be plotted.
 Accepts the same location keywords as <code><a rd-options='graphics' href='legend'>legend</a></code>

is a graphical parameter setting the plot use lines, points 
 or both (see <code><a rd-options='' href='plot'>plot</a></code>).

plot.eff: Plot `eff` objects

Description

Usage

Arguments

Value

Details

References

See Also