AffyExonPDInfoPkgSeed-class

AffyGenePDInfoPkgSeed-class

	 container for parameters related to pdmapping package construction for ST type arrays

classes

AffySTPDInfoPkgSeed-class

Builds platform design information packages.
These consist of a SQLite database containing feature-level
data such as x, y position on chip and
featureSet ID. The database also incorporates featureSet-level
annotation data. The products of this packages are used by the oligo pkg.

Benilton Carvalho

pdInfoBuilder

Platform Design Information Package Builder

AffySTPDInfoPkgSeed-class function

Objects can be created by calls of the form <code>new("AffySTPDInfoPkgSeed", pgfFile, clfFile, probeFile, transFile, ...)</code>.

Objects from the Class

<dl>
    <dt><code>pgfFile</code>:</dt><dd>Object of class <code>"ScalarCharacter"</code> path to pgf </dd> <dt><code>clfFile</code>:</dt><dd>Object of class <code>"ScalarCharacter"</code> path to clf </dd> <dt><code>probeFile</code>:</dt><dd>Object of class <code>"ScalarCharacter"</code>, path to probe sequence file (Optional) </dd> <dt><code>transFile</code>:</dt><dd>Object of class <code>"ScalarCharacter"</code>, path to trans file (Optional) </dd> <dt><code>chipName</code>:</dt><dd>Name of the chip or platform</dd> <dt><code>manufacturer</code>:</dt><dd>chip/platform manufacturer</dd> <dt><code>url</code>:</dt><dd>chip URL</dd> <dt><code>genomebuild</code>:</dt><dd>The genome build this platform is based
      upon.</dd> <dt><code>organism</code>:</dt><dd> organism for chip. </dd> <dt><code>species</code>:</dt><dd> species for chip. </dd> <dt><code>version</code>:</dt><dd>A character vector giving the version
      number of the package.</dd> <dt><code>license</code>:</dt><dd>The license of the package</dd> <dt><code>author</code>:</dt><dd>Author of the package</dd> <dt><code>email</code>:</dt><dd>An email address to use in the Maintainer field</dd> <dt><code>biocViews</code>:</dt><dd>Character data for the biocViews field of
    the DESCRIPTION file</dd> </dl> 

Slots

<dl>
    <dt>chipName</dt><dd><code>signature(object = "AffySTPDInfoPkgSeed")</code>: ... </dd> <dt>getGeometry</dt><dd><code>signature(object = "AffySTPDInfoPkgSeed")</code>: ... </dd> <dt>makePdInfoPackage</dt><dd><code>signature(object = "AffySTPDInfoPkgSeed")</code>: ... </dd> </dl> 

Methods

container for parameters related to pdmapping package construction for ST type arrays

AffySTPDInfoPkgSeed-class: Class "AffySTPDInfoPkgSeed" for the Sense Target gene-level array

Description

Arguments

Objects from the Class

Slots

Methods

Examples