coerce-methods: Coerce a maiges object to classes defined by packages limma...

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

Coercing methods were defined to convert maiges objects of classes maiges and maigesRaw into objects of classes marrayNorm and marrayRaw from package marray or classes MAList and RGList from package limma and vice-versa.

Usage

## S4 method for signature 'maiges,marrayNorm'
as(from, to)

## S4 method for signature 'marrayNorm,maiges'
as(from, to)

## S4 method for signature 'maiges,MAList'
as(from, to)

## S4 method for signature 'MAList,maiges'
as(from, to)

## S4 method for signature 'maigesRaw,marrayRaw'
as(from, to)

## S4 method for signature 'marrayRaw,maigesRaw'
as(from, to)

## S4 method for signature 'maigesRaw,RGList'
as(from, to)

## S4 method for signature 'RGList,maigesRaw'
as(from, to)

Arguments

from	object of class maiges, maigesRaw, MAList, RGList, marrayNorm or marrayRaw.
to	character string specifying the class of object to which the object from will be coerced

Details

When converting from objects of classes RGList or marrayRaw to class maigesRaw, the slot Sf and Sb will always receive the channel 2 (red) values, and Rf and Rb will always receive channel 1 (green) values. For the normalized ojects, the slot W will be equivalent to the M values.

When converting from objects of classes maigesRaw or maiges to classes RGList, marrayRaw, MAList or marrayNorm the correct values of the two channels or of M values are calculated.

Methods

from = maiges, to = marrayNorm

convert an object of class maiges into an object of class marrayNorm.

from = marrayNorm, to = maiges

convert an object of class marrayNorm into an object of class maiges.

from = maiges, to = MAList

convert an object of class maiges into an object of class MAList.

from = MAList, to = maiges

convert an object of class MAList into an object of class maiges.

from = maigesRaw, to = marrayRaw

convert an object of class maigesRaw into an object of class marrayRaw.

from = marrayRaw, to = maigesRaw

convert an object of class marrayRaw into an object of class maigesRaw.

from = maigesRaw, to = RGList

convert an object of class maigesRaw into an object of class RGList.

from = RGList, to = maigesRaw

convert an object of class RGList into an object of class maigesRaw.

Note

It is possible to use Package convert to convert objects between classes defined in packages limma, marray and Biobase.

See Also

as in the methods package.

Examples

## Loading the dataset
data(gastro)

## Converting a maigesRaw class object into marrayRaw object
as(gastro.raw, "marrayRaw")

## Converting a maigesRaw class object into RGList
as(gastro.raw, "RGList")

## Converting a maiges class object into marrayNorm object
as(gastro.norm, "marrayNorm")

## Converting a maiges class object into MAList object
as(gastro.summ, "MAList")

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.