These methods link filter descriptions to a particular set of flow cytometry data allowing for the lightweight calculation of summary statistics common to flow cytometry analysis.
Object of class
An object of class
These arguments are not used.
filter method conceptually links a filter description,
represented by a
filter object, to a particular
flowFrame. This is accomplished via the
filterResult object, which tracks the linked
frame as well as caching the results of the filtering operation
itself, allowing for fast calculation of certain summary statistics
such as the percentage of events accepted by the
method exists chiefly to allow the calculation of these statistics
without the need to first
flowFrame, which can be quite large.
When applying on a
filter argument can
either be a single
filter object, in which case it is recycled
for all frames in the set, or a named list of
objects. The names are supposed to match the frame identifiers (i.e.,
the output of
sampleNames(x) of the
flowSet. If some
frames identifiers are missing, the particular frames are skipped
during filtering. Accordingly, all
filters in the filter list
that can't be mapped to the
flowSet are ignored. Note that all
filter objects in the list must be of the same type,
filterResult object or a
filterResultList object if
x is a
flowSet. Note that
filterResult objects are themselves filters,
allowing them to be used in filter expressions or
F Hahne, B. Ellis, N. Le Meur
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## Filtering a flowFrame samp <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore")) rectGate <- rectangleGate(filterId="nonDebris","FSC-H"=c(200,Inf)) fr <- filter(samp,rectGate) class(fr) summary(fr) ## filtering a flowSet data(GvHD) foo <- GvHD[1:3] fr2 <- filter(foo, rectGate) class(fr2) summary(fr2) ## filtering a flowSet using different filters for each frame rg2 <- rectangleGate(filterId="nonDebris","FSC-H"=c(300,Inf)) rg3 <- rectangleGate(filterId="nonDebris","FSC-H"=c(400,Inf)) flist <- list(rectGate, rg2, rg3) names(flist) <- sampleNames(foo) fr3 <- filter(foo, flist)
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