quadGate-class: Class "quadGate"

In flowCore: flowCore: Basic structures for flow cytometry data

Description

Class and constructors for quadrant-type filter objects.

Usage

quadGate(..., .gate, filterId="defaultQuadGate")

Arguments

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.

Details

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.

Value

Returns a quadGate object for use in filtering flowFrames or other flow cytometry objects.

Slots

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.

Extends

Class "parameterFilter", directly.

Class "concreteFilter", by class parameterFilter, distance 2.

Class "filter", by class parameterFilter, distance 3.

Objects from the Class

Objects can be created by calls of the form new("quadGate", ...) or using the constructor quadGate. The latter is the recommended way.

Methods

%in%

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.

show

signature(object = "quadGate"): Print information about the gate.

Note

See the documentation in the flowViz package for plotting of quadGates.

Author(s)

F.Hahne, B. Ellis N. Le Meur

See Also

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

Examples

## 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+")))

flowCore documentation built on Nov. 8, 2020, 5:19 p.m.