AlleleSetIllumina-class

initialize,AlleleSetIllumina-method

Container for high-throughput assays and experimental
  metadata. <code>"AlleleSetIllumina"</code> class is derived from
  <code>"<a href="/link/eSet?package=beadarrayMSV&version=1.1.0&to=Biobase%3AeSet" rd-options="Biobase:eSet" data-mini-rdoc="Biobase:eSet::eSet">eSet</a>"</code> and requires matrices
  <dquote>intensity</dquote>, <dquote>theta</dquote>, and <dquote>SE</dquote> as assay data
  members

classes

Imports bead-summary data from Illumina scanner.
Pre-processes using a suite of optional normalizations and
transformations. Clusters and automatically calls genotypes,
critically able to handle markers in duplicated regions of the
genome (multisite variants; MSVs). Interactive clustering if
needed. MSVs with variation in both paralogs may be resolved
and mapped to their respective chromosomes. Quality control
including pedigree checking and visual assessment of clusters.
Too large data-sets are handled by working on smaller subsets
of the data in sequence.

Lars Gidskehaug

beadarrayMSV

Analysis of Illumina BeadArray SNP data including MSV markers

AlleleSetIllumina-class function

<code>new("AlleleSetIllumina", ...)</code>
  
  <code>new("AlleleSetIllumina", phenoData = [AnnotatedDataFrame],
    featureData = [AnnotatedDataFrame], experimentData = [MIAME],
    annotation = [character], intensity = [matrix], theta = [matrix],
    SE = [matrix], ...)</code>
  
  Most arguments are optional, however usually the arguments to <code>new</code>
  include at least <dquote>intensity</dquote>, <dquote>theta</dquote>, and <dquote>SE</dquote>. Note
  that several methods requires additional <code>assayData</code>,
  <code>phenoData</code>, or <code>featureData</code> entries<p></p><p>  <code>"AlleleSetIllumina"</code> instances are usually created from
  <code>"<links4class>BeadSetIllumina</links4class>"</code> instances using
  <code><a href="/link/createAlleleSet?package=beadarrayMSV&version=1.1.0" rd-options="" data-mini-rdoc="beadarrayMSV::createAlleleSet">createAlleleSet</a></code> or from text-files using
  <code><a href="/link/createAlleleSetFromFiles?package=beadarrayMSV&version=1.1.0" rd-options="" data-mini-rdoc="beadarrayMSV::createAlleleSetFromFiles">createAlleleSetFromFiles</a></code></p>

Objects from the Class

Class <code>"<links4class>eSet</links4class>"</code>, directly.
  Class <code>"<links4class>VersionedBiobase</links4class>"</code>, by class <code>"eSet"</code>, distance 2.
  Class <code>"<links4class>Versioned</links4class>"</code>, by class <code>"eSet"</code>, distance 3.

AlleleSetIllumina-class: Class to Contain Objects Describing High-Throughput Illumina BeadArrays

Description

Arguments

Objects from the Class

Extends

See Also

Examples