GeneAcceptFilter: The GeneAcceptFilter class

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Package: aroma
Class GeneAcceptFilter

Object
~~|
~~+--Filter
~~~~~~~|
~~~~~~~+--SerialFilter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AcceptFilter
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GeneAcceptFilter

Directly known subclasses:

public static class GeneAcceptFilter
extends AcceptFilter

An GeneAcceptFilter asks its input for indices and let only those indices through that corresponds to a given set of genes.

Usage

GeneAcceptFilter(input, layout, genes=NULL, ids=NULL, names=NULL, ...)

Arguments

input	The input Filter to be connected to.
layout	A Layout object.
genes	Gene

.

ids

.

names

.

...	Any arguments accepted by the AcceptFilter constructor.

Either 'genes', 'ids' or 'names' must be given.

Fields and Methods

Methods:

	as.character	-
	getIndex	-

Methods inherited from AcceptFilter:
getIndex

Methods inherited from SerialFilter:
changeInput, getInput

Methods inherited from Filter:
as.character, changeInput, getIndex, getInput, getParameter, getVisible, highlight, setParameter, setVisible, text

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

See Also

See also the AcceptFilter class.

Examples

   SMA$loadData("mouse.data")
   layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))
   raw <- RawData(mouse.data, layout=layout)

   ma <- getSignal(raw)
   normalizeWithinSlide(ma, "s")
   normalizeAcrossSlides(ma)

   tma <- as.TMAData(ma)

   # Look at the top 5% extreme M values
   fM  <- MFilter(tma, top=0.05, col="red")

   # And among those only look at the duplicated genes.
   genes <- getGeneGroups(layout)
   duplicates <- which(getSizes(genes) == 2)
   myFilter <- GeneAcceptFilter(fM, layout=layout, genes=duplicates, col="blue")
   plot(tma)
   highlight(myFilter, recursive=TRUE)

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.