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.

- %in%
`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.- show
`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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