Class and constructor for data-driven
that discard margin events.
Character giving the name(s) of the measurement parameter(s) on
which the filter is supposed to work. Note that all events on the
margins of ay of the channels provided by
Numeric vector, used to set the
Character vector, used to set the
An optional parameter that sets the
Flow cytomtery instruments usually operate on a given data range, and
the limits of this range are stored as keywords in the FSC
files. Depending on the amplification settings and the dynamic range
of the measured signal, values can occur that are outside of the
measurement range, and most instruments will simply pile those values
at the minimum or maximum range limit. The
removes these values, either for a single parameter, or for a
combination of parameters. Note that it is often desirable to treat
boundary events on a per-parameter basis, since their values might be
uninformative for one particular channel, but still be useful in all of
the other channels.
boundaryFilter is a convenience function for
object instantiation. Evaluating a
boundaryFilter results in a
single sub-populations, an hence in an object of class
boundaryFilter object for use in filtering
flowFrames or other flow cytometry objects.
"concreteFilter", by class
parameterFilter, distance 2.
"filter", by class
Object of class
machine tolerance used to decide whether an event is on the
measurement boundary. Essentially, this is done by evaluating
x>minRange+tolerance & x<maxRange-tolerance.
Object of class
"character". The margin
on which to evaluate the filter. Either
upper for the
upper margin or
lower for the lower margin or
for both margins.
Objects can be created by calls of the form
...) or using the constructor
boundaryFilter. Using the
constructor is the recommended way of object instantiation:
signature(x = "flowFrame", table =
"boundaryFilter"): The workhorse used to evaluate the filter on
data. This is usually not called directly by the user, but
internally by calls to the
signature(object = "boundaryFilter"): Print
information about the filter.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## Loading example data dat <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore")) ## Create directly. Most likely from a command line boundaryFilter("FSC-H", filterId="myBoundaryFilter") ## To facilitate programmatic construction we also have the following bf <- boundaryFilter(filterId="myBoundaryFilter", x=c("FSC-H")) ## Filtering using boundaryFilter fres <- filter(dat, bf) fres summary(fres) ## We can subset the data with the result from the filtering operation. Subset(dat, fres) ## A boundaryFilter on the lower margins of several channels bf2 <- boundaryFilter(x=c("FSC-H", "SSC-H"), side="lower")
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