Description Usage Arguments Details Value Slots Extends Objects from the Class Methods Note Author(s) See Also Examples
Class and constructor for n-dimensional 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.
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.
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("ellipsoidGate",
...)
or by using the constructor ellipsoidGate
. Using the
constructor is the recommended way.
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.
Other Gate classes:
polygonGate-class
,
polytopeGate-class
,
quadGate-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 | ## 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("FSC-H", "SSC-H"), c("FSC-H", "SSC-H")))
mean <- c("FSC-H"=430, "SSC-H"=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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