Class and constructor for data-driven
filter objects 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
boundaryFilter 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.
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.
"concreteFilter", by class
parameterFilter, distance 2.
"filter", by class
Objects can be created by calls of the form
...) or using the constructor
boundaryFilter. Using the
constructor is the recommended way.
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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