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

Description Usage Arguments Fields and Methods Author(s) See Also Examples

Package: aroma
Class SerialFilter

Object
~~|
~~+--Filter
~~~~~~~|
~~~~~~~+--SerialFilter

Directly known subclasses:
AcceptFilter, AFilter, BFilter, DfFilter, FieldFilter, GeneAcceptFilter, GeneRejectFilter, MFilter, NotFilter, RejectFilter, SEFilter, TFilter

public abstract static class SerialFilter
extends Filter

A SerialFilter is a filter that passes through indices from a single input given some criteria.

1	SerialFilter(input=NULL, ...)

`input`	The input `Filter` to be connected to.
`...`	Any arguments accepted by the `Filter` constructor.

Fields

	input	The input.

Methods:

	`changeInput`	Change input(s) on this filter and optionally all filters down the stream.
	`getInput`	Gets all the input objects connected to the filter.

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

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

See also the ParallelFilter class.

   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)

   fM  <- MFilter(tma, top=0.05, col="red")
   fT  <- TFilter(tma, top=0.05, col="blue")
   fNotSE <- SEFilter(tma, range=c(-Inf,0.02), col="yellow")
   fSE <- NotFilter(fNotSE, visible=FALSE)
   myFilter <- AndFilter(fM, fT, fSE, col="purple")

   plot(tma, "TvsSE")
   highlight(myFilter, recursive=TRUE)