flowStats (version 3.30.0)

lymphFilter-class: Automated gating of elliptical cell populations in 2D.

Description

Cell populations of roughly elliptical shape in two-dimensional projections are of huge interest in many flow cytometry applications. This function identifies a single such population, potentially from a mixture of multiple populations.

Usage

lymphGate(x, channels, preselection=NULL, scale=2.5,  bwFac=1.3, filterId="defaultLymphGate", evaluate=TRUE, plot=FALSE, ...)

Arguments

x

An object of class flowSet.

channels

A character vector of length 2 of valid flow parameters in x.

preselection

Either NULL, in which case this boils down to fitting a regular norm2Filter, a character scalar giving one of the flow parameters in x, or a named list of numerics specifying the initial rough preselection. The latter gets passed on to rectangleGate, see it's documentation for details.

scale

The scaleFactor parameter that gets passed on to norm2Filter.

bwFac

The bandwidth factor that gets passed on to curv1Filter.

filterId

A character used as filterId.

evaluate

A logical indicating wether the filter should be resolved (computation of the filterResult and the subset).

plot

Logical. Produce plots of filter results

...

Additional arguments.

Value

A list with items

x

The filtered flowSet.

n2gate

The norm2Filter object.

n2gateResults

The filterResult after applying the norm2Filter on the flowSet.

for the lymphGate function. Note that x and n2gateResults are NULL when eval=FALSE.

Extends

Class parameterFilter, directly. Class concreteFilter, by class "parameterFilter", distance 2. Class filter, by class "parameterFilter", distance 3.

Slots

See Arguments section for details.

preselection:

Object of class character, the name of the flow parameter used for preselection.

rectDef:

Object of class list, the initial rectangular selection.

scale:

Object of class numeric.

bwFac:

Object of class numeric.

parameters:

Object of class parameters, the flow parameters to operate on.

filterId:

Object of class "character", the filter identifier.

Objects from the Class

Objects can be created by calls of the form new("lymphFilter", parameters, ...) or using the constructor lymphFilter. The constructor is the recommended way of object instantiation.

Details

This algorithm does not apply real mixture modelling, however it is able to identify a single elliptical cell population from a mixture of multiple such populations. The idea is to first define a rough rectangular preselection and, in a second step, fit a bivariate normal distribution to this subset only.

Depending on the value of preselection, the initial rough selection is either

NULL:

No preselection at all

character scalar

Preselection based on cells that are positive for a single marker only. This allows for back-gating, for instances by selecting CD4+ T-cells and using this information to back-gate lymphocytes in FSC and SSC. Positive cells are identified using a curv1Filter.

a named list of numerics:

Preselection by a rectangular gate. The items of the list have to be numerics of length one giving the gate boundaries in the respective dimensions.

See Also

norm2Filter, curv1Filter

Examples

data(GvHD)
dat <- GvHD[pData(GvHD)$Patient==10]
dat <- transform(dat, "FL4-H"=asinh(`FL4-H`))
lg <- lymphGate(dat, channels=c("FSC-H", "SSC-H"), preselection="FL4-H",scale=1.5)

if(require(flowViz))
xyplot(`SSC-H`~`FSC-H`, dat, filter=lg$n2gate)