gArray-class

dim,gArray-method

getLayout,gArray-method

metadata<-,gArray-method

metadata,gArray-method

ncol,gArray-method

nrow,gArray-method

getLayout

metadata<-

metadata


  The virtual class <code>gArray</code> is used to stadarize the storage and  access of array-like experiment arrangement.It represent the  arrangement of the experiment units, such as slide ans plate.<p></p><p></p>

classes

A sizable genomics study such as microarray often involves
the use of multiple batches (groups) of experiment due to
practical complication. To minimize batch effects, a careful
experiment design should ensure the even distribution of
biological groups and confounding factors across batches. OSAT
(Optimal Sample Assignment Tool) is developed to facilitate the
allocation of collected samples to different batches. With
minimum steps, it produces setup that optimizes the even
distribution of samples in groups of biological interest into
different batches, reducing the confounding or correlation
between batches and the biological variables of interest. It
can also optimize the even distribution of confounding factors
across batches. Our tool can handle challenging instances where
incomplete and unbalanced sample collections are involved as
well as ideal balanced RCBD. OSAT provides a number of
predefined layout for some of the most commonly used genomics
platform. Related paper can be find at
http://www.biomedcentral.com/1471-2164/13/689 .

Li Yan

OSAT

OSAT: Optimal Sample Assignment Tool

gArray-class function

A virtual Class: No objects may be created from it.

Objects from the Class

<dl>
    <dt><code>nRows</code>:</dt><dd>Object of class <code>"integer"</code>. Number of
      units per row. </dd> <dt><code>nColumns</code>:</dt><dd>Object of class <code>"integer"</code>. Number of
      units per column. </dd> <dt><code>layout</code>:</dt><dd>Object of class <code>"data.frame"</code>. A data
      frame represent the layout and order of postiion. </dd> <dt><code>byrow</code>:</dt><dd>Object of class <code>"logical"</code>. The order of
      position is filled by row or not. Default is FALSE, same as
      used in mactrix().  </dd> <dt><code>metadata</code>:</dt><dd>Object of class <code>"list"</code>. A list that
      holds brief description of the class and other information. </dd> </dl> 

Slots

In the following code snippets, <code>x</code> is an <code>gArray</code> object. <dl>
    <dt>dim</dt><dd><code>signature(x = "gArray")</code>: Return the dimmension of
    the array. </dd> <dt>getLayout</dt><dd><code>signature(x = "gArray")</code>: Return a data frame
    represent the layout postions of the array.</dd> <dt>metadata&lt;-</dt><dd><code>signature(x = "gArray")</code>: Set the metadata. </dd> <dt>metadata</dt><dd><code>signature(x = "gArray")</code>: Get the metadata. </dd> <dt>ncol</dt><dd><code>signature(x = "gArray")</code>: Return the number of columns.</dd> <dt>nrow</dt><dd><code>signature(x = "gArray")</code>: Return the number of rows. </dd> </dl> 

Methods

The virtual class <code>gArray</code> is used to stadarize the storage and  access of array-like experiment arrangement.It represent the  arrangement of the experiment units, such as slide ans plate.

gArray-class: Class `"gArray"`

Description

Arguments

Objects from the Class

Slots

Methods