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
filter. This method exists chiefly to allow
the calculation of these statistics without the need to first
flowFrame, which can be quite
When applying on a
filter argument can either be
filter object, in which case it is recycled for all frames
in the set, or a named list of
filter objects. The names are supposed
to match the frame identifiers (i.e., the output of
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
filter objects in the list must be of the same type, e.g.
filterResult object or a
filterResultList object if
x is a
flowSet. Note that
objects are themselves filters, allowing them to be used in filter
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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