eff-class

show.eff

show,eff-method

summary.eff

summary,eff-method

An S4 class containing the output <code><a rd-options="" href="/link/effcalc?package=chipPCR&version=1.0-2" data-mini-rdoc="chipPCR::effcalc">effcalc</a></code> function.

classes

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

eff function

<dl class="dl-horizontal">
 <dt><code>.Data</code>:</dt><dd><code>"matrix"</code> containing the "Concentration", "Location" 
 (mean, median), "Deviation" (standard deviation, median absolute 
 deviation), "Coefficient of Variance" (CV, RSD) sequential in the 
 columns.</dd>
 <dt><code>amplification.efficiency</code>:</dt><dd><code>"numeric"</code> value representing 
 amplification efficiency.</dd>
 <dt><code>regression</code>:</dt><dd><code>"lm"</code> the results of the linear regression and .</dd>
 <dt><code>correlation.test</code>:</dt><dd><code>"htest"</code>. the correlation test 
 (Pearson) results.</dd>
</dl>

Slots

<dl class="dl-horizontal">
 <dt>plot</dt><dd><code>signature(x = "eff")</code>: plots calculated efficiency. 
 See <code><a rd-options="" href="/link/plot.eff?package=chipPCR&version=1.0-2" data-mini-rdoc="chipPCR::plot.eff">plot.eff</a></code></dd>
 <dt>show</dt><dd><code>signature(object = "eff")</code>: prints only <code>.Data</code> slot of the
 object.</dd>
 <dt>summary</dt><dd><code>signature(object = "eff")</code>: prints information about object 
 prettier than <code>show</code>.</dd></dl>

Methods

An S4 class containing the output <code><a rd-options='' href='effcalc'>effcalc</a></code> function.

Class <code>"eff"</code> — eff

<dl class='dl-horizontal'>
 <dt><code>.Data</code>:</dt><dd><code>"matrix"</code> containing the "Concentration", "Location" 
 (mean, median), "Deviation" (standard deviation, median absolute 
 deviation), "Coefficient of Variance" (CV, RSD) sequential in the 
 columns.</dd>
 <dt><code>amplification.efficiency</code>:</dt><dd><code>"numeric"</code> value representing 
 amplification efficiency.</dd>
 <dt><code>regression</code>:</dt><dd><code>"lm"</code> the results of the linear regression and .</dd>
 <dt><code>correlation.test</code>:</dt><dd><code>"htest"</code>. the correlation test 
 (Pearson) results.</dd>
</dl>

eff: Class `"eff"`

Description

Arguments

Slots

Methods

See Also