AcceptFilter: The AcceptFilter 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 AcceptFilter

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

Directly known subclasses:
GeneAcceptFilter

public static class AcceptFilter
extends SerialFilter

An AcceptFilter asks its input for indices and let only those indices through that is specified by its field accept.

1	AcceptFilter(input, accept=NULL, ...)

`input`	The input `MicroarrayData` object.
`accept`	Vector of spot indices to be accepted.
`...`	Other arguments accepted by the constructor of the `SerialFilter` class.

Methods:

	`getIndex`	Gets indices accepted by this filter.

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 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)

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

   # And among those only look at the first 1000 spots.
   myFilter <- AcceptFilter(fM, accept=1:1000)

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