FieldFilter: The FieldFilter class

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

Description

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.

Usage

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

Arguments

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 and Methods

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

Author(s)

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

See Also

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

Examples

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   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);

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