th-class

summary.th

summary,th-method

show.th

show,th-method

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

th function

<dl class="dl-horizontal">
 <dt><code>.Data</code>:</dt><dd><code>"matrix"</code> is a matrix containing the 
 		 threshold cycle and threshold fluorescence.</dd>
 <dt><code>stats</code>:</dt><dd><code>"summary.lm"</code> contains linear model used for Ct estimation.</dd>
 <dt><code>input</code>:</dt><dd><code>"matrix"</code> input data for linear model.</dd>
</dl>

Slots

<dl class="dl-horizontal">
 <dt>summary</dt><dd><code>signature(object = "th")</code>: prints summary 
		 of the object.</dd>
 <dt>show</dt><dd><code>signature(object = "th")</code>: prints only 
		<code>.Data</code> slot of the object.</dd>
 </dl>

Methods

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

Class <code>"th"</code> — th

<dl class='dl-horizontal'>
 <dt><code>.Data</code>:</dt><dd><code>"matrix"</code> is a matrix containing the 
 		 threshold cycle and threshold fluorescence.</dd>
 <dt><code>stats</code>:</dt><dd><code>"summary.lm"</code> contains linear model used for Ct estimation.</dd>
 <dt><code>input</code>:</dt><dd><code>"matrix"</code> input data for linear model.</dd>
</dl>

<dl class='dl-horizontal'>
 <dt>summary</dt><dd><code>signature(object = "th")</code>: prints summary 
		 of the object.</dd>
 <dt>show</dt><dd><code>signature(object = "th")</code>: prints only 
		<code>.Data</code> slot of the object.</dd>
 </dl>

th: Class `"th"`

Description

Arguments

Value

Slots

Methods

See Also

Examples