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=0.0.8-10&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.

Stefan Roediger

chipPCR

Toolkit of Helper Functions to Pre-Process Amplification Data

th function

<dl>
    <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>
    <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

Slots

Methods

See Also

Examples