runType

A run is a set of reactions performed in one "run", for example one plate,
one rotor, one array, one chip. Inherits: <a rd-options="" href="/link/rdmlBaseType?package=RDML&version=1.0" data-mini-rdoc="RDML::rdmlBaseType">rdmlBaseType</a>.

datasets

Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) and transforms to the appropriate formats of
the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization
for the structure of RDML object and GUI for RDML editing.

Konstantin A Blagodatskikh

RDML

Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files

Konstantin A. Blagodatskikh

Stefan Roediger

Michal Burdukiewicz

Andrej-Nikolai Spiess

runType function

An <code><a rd-options="" href="/link/R6Class?package=RDML&version=1.0" data-mini-rdoc="RDML::R6Class">R6Class</a></code> generator object.

Format

<pre>runType$new(id, description = NULL,
 documentation = NULL, experimenter = NULL, instrument = NULL,
 dataCollectionSoftware = NULL, backgroundDeterminationMethod = NULL,
 cqDetectionMethod = NULL, thermalCyclingConditions = NULL, pcrFormat,
 runDate = NULL, react = NULL)</pre>

Initialization

<dl class="dl-horizontal">
 <dt><code>id</code></dt><dd><a rd-options="" href="/link/idType?package=RDML&version=1.0" data-mini-rdoc="RDML::idType">idType</a>.</dd>
 <dt><code>description</code></dt><dd><a rd-options="checkmate" href="/link/checkString?package=RDML&version=1.0&to=checkmate" data-mini-rdoc="checkmate::checkString">checkString</a>.</dd>
 <dt><code>documentation</code></dt><dd><code>list</code> of <a rd-options="" href="/link/idReferencesType?package=RDML&version=1.0" data-mini-rdoc="RDML::idReferencesType">idReferencesType</a>.</dd>
 <dt><code>experimenter</code></dt><dd><code>list</code> of <a rd-options="" href="/link/idReferencesType?package=RDML&version=1.0" data-mini-rdoc="RDML::idReferencesType">idReferencesType</a>.</dd>
 <dt><code>instrument</code></dt><dd><a rd-options="checkmate" href="/link/checkString?package=RDML&version=1.0&to=checkmate" data-mini-rdoc="checkmate::checkString">checkString</a>. Description of the
 instrument used to aquire the data.</dd>
 <dt><code>dataCollectionSoftware</code></dt><dd><a rd-options="" href="/link/dataCollectionSoftwareType?package=RDML&version=1.0" data-mini-rdoc="RDML::dataCollectionSoftwareType">dataCollectionSoftwareType</a>.
 Description of the software used to analyze/collect the data.</dd>
 <dt><code>backgroundDeterminationMethod</code></dt><dd><a rd-options="checkmate" href="/link/checkString?package=RDML&version=1.0&to=checkmate" data-mini-rdoc="checkmate::checkString">checkString</a>.
 Description of method used to determine the background.</dd>
 <dt><code>cqDetectionMethod</code></dt><dd><a rd-options="" href="/link/cqDetectionMethodType?package=RDML&version=1.0" data-mini-rdoc="RDML::cqDetectionMethodType">cqDetectionMethodType</a>. Description of method
 used to calculate the quantification cycle.</dd>
 <dt><code>thermalCyclingConditions</code></dt><dd><a rd-options="" href="/link/idReferencesType?package=RDML&version=1.0" data-mini-rdoc="RDML::idReferencesType">idReferencesType</a>. The program
 used to aquire the data.</dd>
 <dt><code>pcrFormat</code></dt><dd><a rd-options="" href="/link/adpsType?package=RDML&version=1.0" data-mini-rdoc="RDML::adpsType">adpsType</a>.</dd>
 <dt><code>runDate</code></dt><dd><a rd-options="" href="/link/adpsType?package=RDML&version=1.0" data-mini-rdoc="RDML::adpsType">adpsType</a>. Time stamp of data acquisition.</dd>
 <dt><code>react</code></dt><dd><code>list</code> of <a rd-options="" href="/link/adpsType?package=RDML&version=1.0" data-mini-rdoc="RDML::adpsType">adpsType</a>.</dd> </dl>

Fields

<dl class="dl-horizontal">
 <dt><code>AsDataFrame(dp.type = "adp")</code></dt><dd>Represents amplification
 (<code>dp.type = "adp"</code>) or melting (<code>dp.type = "mdp"</code>) data
 points as <code>data.frame</code></dd></dl>

Methods

A run is a set of reactions performed in one "run", for example one plate,
one rotor, one array, one chip. Inherits: <a rd-options='' href='rdmlBaseType'>rdmlBaseType</a>.

runType R6 class. — runType

An <code><a rd-options='' href='R6Class'>R6Class</a></code> generator object.

<dl class='dl-horizontal'>
 <dt><code>id</code></dt><dd><a rd-options='' href='idType'>idType</a>.</dd>
 <dt><code>description</code></dt><dd><a rd-options='checkmate' href='checkString'>checkString</a>.</dd>
 <dt><code>documentation</code></dt><dd><code>list</code> of <a rd-options='' href='idReferencesType'>idReferencesType</a>.</dd>
 <dt><code>experimenter</code></dt><dd><code>list</code> of <a rd-options='' href='idReferencesType'>idReferencesType</a>.</dd>
 <dt><code>instrument</code></dt><dd><a rd-options='checkmate' href='checkString'>checkString</a>. Description of the
 instrument used to aquire the data.</dd>
 <dt><code>dataCollectionSoftware</code></dt><dd><a rd-options='' href='dataCollectionSoftwareType'>dataCollectionSoftwareType</a>.
 Description of the software used to analyze/collect the data.</dd>
 <dt><code>backgroundDeterminationMethod</code></dt><dd><a rd-options='checkmate' href='checkString'>checkString</a>.
 Description of method used to determine the background.</dd>
 <dt><code>cqDetectionMethod</code></dt><dd><a rd-options='' href='cqDetectionMethodType'>cqDetectionMethodType</a>. Description of method
 used to calculate the quantification cycle.</dd>
 <dt><code>thermalCyclingConditions</code></dt><dd><a rd-options='' href='idReferencesType'>idReferencesType</a>. The program
 used to aquire the data.</dd>
 <dt><code>pcrFormat</code></dt><dd><a rd-options='' href='adpsType'>adpsType</a>.</dd>
 <dt><code>runDate</code></dt><dd><a rd-options='' href='adpsType'>adpsType</a>. Time stamp of data acquisition.</dd>
 <dt><code>react</code></dt><dd><code>list</code> of <a rd-options='' href='adpsType'>adpsType</a>.</dd> </dl>

<dl class='dl-horizontal'>
 <dt><code>AsDataFrame(dp.type = "adp")</code></dt><dd>Represents amplification
 (<code>dp.type = "adp"</code>) or melting (<code>dp.type = "mdp"</code>) data
 points as <code>data.frame</code></dd></dl>

runType: runType R6 class.

Description

Usage

Arguments

Format

Initialization

Fields

Methods