Description Usage Arguments Fields and Methods Author(s) See Also Examples
Package: aroma
Class GeneAcceptFilter
Object
~~|
~~+--
Filter
~~~~~~~|
~~~~~~~+--
SerialFilter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AcceptFilter
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GeneAcceptFilter
Directly known subclasses:
public static class GeneAcceptFilter
extends AcceptFilter
An GeneAcceptFilter asks its input for indices and let only those indices through that corresponds to a given set of genes.
1 |
input |
The input |
layout |
A |
genes |
Gene |
.
ids |
.
names |
.
... |
Any arguments accepted by the |
Either 'genes', 'ids' or 'names' must be given.
Methods:
as.character | - | |
getIndex | - | |
Methods inherited from AcceptFilter:
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:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save
Henrik Bengtsson (http://www.braju.com/R/)
See also the AcceptFilter
class.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | SMA$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 duplicated genes.
genes <- getGeneGroups(layout)
duplicates <- which(getSizes(genes) == 2)
myFilter <- GeneAcceptFilter(fM, layout=layout, genes=duplicates, col="blue")
plot(tma)
highlight(myFilter, recursive=TRUE)
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