quadGate-class {flowCore} | R Documentation |
Class and constructors for quadrant-type filter
objects.
quadGate(..., .gate, filterId="defaultQuadGate")
filterId |
An optional parameter that sets the filterId
of this filter . The object can later be identified by
this name. |
.gate |
A definition of the gate for programmatic access. This can be either a named list or a named numeric vector, as described below. |
... |
The parameters of quadGates can also be directly
described using named function arguments, as described below. |
quadGates
are defined by two parameters, which specify a
separation of a two-dimensional parameter space into four
quadrants. The quadGate
function is designed to be useful in
both direct and programmatic usage:
For the interactive use, these parameters can be given as additional
named function arguments, where the names correspond to valid
parameter names in a flowFrame
or
flowSet
. For a more programmatic approach, a named list
or numeric vector of the gate boundaries can be passed on to the
function as argument .gate
.
Evaluating a quadGate
results in four sub-populations, and hence
in an object of class multipleFilterResult
. Accordingly,
quadGates
can be used to split flow cytometry data sets.
Returns a quadGate
object for use in filtering
flowFrame
s or other flow cytometry objects.
Class "parameterFilter"
, directly.
Class "concreteFilter"
, by class
parameterFilter
, distance 2.
Class "filter"
, by class parameterFilter
,
distance 3.
boundary
:"numeric"
, length
2. The boundaries of the quadrant regions.parameters
:"character"
,
describing the parameter used to filter the flowFrame
. filterId
:"character"
,
referencing the gate.
Objects can be created by calls of the form new("quadGate",
...)
or using the constructor quadGate
. The latter is the
recommended way of object instantiation:
signature(x = "flowFrame", table =
"quadGate")
: The workhorse used to evaluate the gate on
data. This is usually not called directly by the user, but
internally by calls to the filter
methods. signature(object = "quadGate")
: Print
information about the gate.
See the documentation in the
flowViz
package for plotting of
quadGates
.
F.Hahne, B. Ellis N. Le Meur
flowFrame
, flowSet
, filter
for evaluation of quadGates
and split
for
splitting of flow cytometry data sets based on that.
## Loading example data dat <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore")) ## Create directly. Most likely from a command line quadGate(filterId="myQuadGate1", "FSC-H"=100, "SSC-H"=400) ## To facilitate programmatic construction we also have the following quadGate(filterId="myQuadGate2", list("FSC-H"=100, "SSC-H"=400)) ## FIXME: Do we want this? ##quadGate(filterId="myQuadGate3", .gate=c("FSC-H"=100, "SSC-H"=400)) ## Filtering using quadGates qg <- quadGate(filterId="quad", "FSC-H"=600, "SSC-H"=400) fres <- filter(dat, qg) fres summary(fres) names(fres) ## The result of quadGate filtering are multiple sub-populations ## and we can split our data set accordingly split(dat, fres) ## We can limit the splitting to one or several sub-populations split(dat, fres, population="FSC-H-SSC-H-") split(dat, fres, population=list(keep=c("FSC-H-SSC-H-", "FSC-H-SSC-H+")))