filter {flowCore} | R Documentation |
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.
filter(x, filter, method = c("convolution", "recursive"), sides = 2L, circular = FALSE, init = NULL)
x |
|
filter |
An object of class |
method,sides,circular,init |
These arguments are not used. |
The 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 Subset
a
flowFrame
, which can be quite large.
When applying on a flowSet
, the 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 filter
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,
e.g. rectangleGates
.
A 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 Subset
operations.
F Hahne, B. Ellis, N. Le Meur
## 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)