GeneRejectFilter: The GeneRejectFilter 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 GeneRejectFilter

Object
~~|
~~+--Filter
~~~~~~~|
~~~~~~~+--SerialFilter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RejectFilter
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GeneRejectFilter

Directly known subclasses:

public static class GeneRejectFilter
extends RejectFilter

An GeneRejectFilter asks its input for indices and let only those indices through that do not corresponds to a given set of genes.

1	GeneRejectFilter(input, layout, genes=NULL, ids=NULL, names=NULL, ...)

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

ids

names

...

Any arguments accepted by the RejectFilter constructor.

Methods:

	`as.character`	-
	`getIndex`	-

Methods inherited from RejectFilter:
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

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

See also the RejectFilter 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)

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

   # However, the blanks, e.g. empty spots, are not of interest
   myFilter <- GeneRejectFilter(fM, layout=layout, ids="BLANK", col="orange")

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