Description Usage Arguments Details Value Extends Slots Objects from the Class Methods Note Author(s) See Also Examples
Class and constructor for ndimensional ellipsoidal
filter
objects.
1  ellipsoidGate(..., .gate, mean, distance=1, filterId="defaultEllipsoidGate")

filterId 
An optional parameter that sets the 
.gate 
A definition of the gate via a covariance matrix. 
mean 
Numeric vector of equal length as dimensions in

distance 
Numeric scalar giving the Mahalanobis distance
defining the size of the ellipse. This mostly exists for
compliance reasons to the gatingML standard as 
... 
You can also directly describe the covariance matrix through named arguments, as described below. 
A convenience method to facilitate the construction of a ellipsoid
filter
objects. Ellipsoid gates in n dimensions (n >= 2)
are specified by a a covarinace matrix and a vector of mean values
giving the center of the ellipse.
This function is designed to be useful in both direct and programmatic usage. In the first case, simply describe the covariance matrix through named arguments. To use this function programmatically, you may pass a covarince matrix and a mean vector directly, in which case the parameter names are the colnames of the matrix.
Returns a ellipsoidGate
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.
mean
:Objects of class "numeric"
. Vector giving
the location of the center of the ellipse in n dimensions.
cov
:Objects of class "matrix"
. The covariance
matrix defining the shape of the ellipse.
distance
:Objects of class "numeric"
. The
Mahalanobis distance defining the size of the ellipse.
parameters
:Object of class "character"
,
describing the parameter used to filter the flowFrame
.
filterId
:Object of class "character"
,
referencing the filter.
Objects can be created by calls of the form new("ellipsoidGate",
...)
or by using the constructor ellipsoidGate
. Using the
constructor is the recommended way of object instantiation:
signature(x = "flowFrame", table =
"ellipsoidGate")
: The workhorse used to evaluate the filter on
data. This is usually not called directly by the user, but
internally by calls to the filter
methods.
signature(object = "ellipsoidGate")
: Print
information about the filter.
See the documentation in the
flowViz
package for plotting of
ellipsoidGates
.
F.Hahne, B. Ellis, N. LeMeur
flowFrame
, polygonGate
,
rectangleGate
, polytopeGate
,
filter
for evaluation of rectangleGates
and
split
and Subset
for splitting and
subsetting of flow cytometry data sets based on that.
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  ## Loading example data
dat < read.FCS(system.file("extdata","0877408774.B08",
package="flowCore"))
## Defining the gate
cov < matrix(c(6879, 3612, 3612, 5215), ncol=2,
dimnames=list(c("FSCH", "SSCH"), c("FSCH", "SSCH")))
mean < c("FSCH"=430, "SSCH"=175)
eg < ellipsoidGate(filterId= "myEllipsoidGate", .gate=cov, mean=mean)
## Filtering using ellipsoidGates
fres < filter(dat, eg)
fres
summary(fres)
## The result of ellipsoid filtering is a logical subset
Subset(dat, fres)
## We can also split, in which case we get those events in and those
## not in the gate as separate populations
split(dat, fres)
##ellipsoidGate can be converted to polygonGate by interpolation
pg < as(eg, "polygonGate")
pg

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