FieldFilter: The FieldFilter 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 FieldFilter

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

Directly known subclasses:
AFilter, BFilter, DfFilter, MFilter, SEFilter, TFilter

public static class FieldFilter
extends SerialFilter

A FieldFilter provides methods to extract indices from MicroarrayData objects given some criteria on one of the fields. Possible criterias on this field are top, and range. The criteria top filters out the top N fraction (or number if N>1). The criteria range filters accepts the spots with a field value within the given range.

1	FieldFilter(mad, field, bottom=NULL, top=NULL, range=NULL, absolute.values=TRUE, cex=NULL, col=NULL, pch=NULL, visible=TRUE)

`mad`	A `MicroarrayData` object to be filtered.
`field`	The field (`character` name) to be filtered.
`top, bottom`	If specified, to top (bottom) values are filtered out. If an `integer` one or greater, that number of indicies will be passed. If a `numeric` between zero and one, that ratio will be passed.
`range`	The range of values to be passed.
`absolute.values`	If `TRUE`, absolute values are filtered, otherwise not.
`cex`	The scale factor of symbols that this filter highlights.
`col`	The color of symbols that this filter highlights.
`pch`	The plot symbols that this filter highlights.
`visible`	If `TRUE`, the data points filtered out by this filter will be highlighted, otherwise not.

Fields

	range	The range criteria.
	top	The top criteria.

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 Filter class. For logical filters see AndFilter, OrFilter, and NotFilter. For data filters see MFilter, AFilter, TFilter and SEFilter.

   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);