Description Usage Arguments Details Value Slots Extends Objects from the Class Methods Note Author(s) See Also Examples
Class and constructors for quadrant-type filter
objects.
1 |
filterId |
An optional parameter that sets the |
.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
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.
boundary
Object of class "numeric"
, length
2. The boundaries of the quadrant regions.
parameters
Object of class "character"
,
describing the parameter used to filter the flowFrame
.
filterId
Object of class "character"
,
referencing the gate.
Class "parameterFilter"
, directly.
Class "concreteFilter"
, by class
parameterFilter
, distance 2.
Class "filter"
, by class parameterFilter
,
distance 3.
Objects can be created by calls of the form new("quadGate",
...)
or using the constructor quadGate
. The latter is the
recommended way.
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.
Other Gate classes:
ellipsoidGate-class
,
polygonGate-class
,
polytopeGate-class
,
rectangleGate-class
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ## 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+")))
|
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