lymphFilter-class | R Documentation |
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.
lymphGate(x, channels, preselection=NULL, scale=2.5, bwFac=1.3,
filterId="defaultLymphGate", plot=FALSE, ...)
x |
An object of class |
channels |
A character vector of length 2 of valid flow
parameters in |
preselection |
Either |
scale |
The |
bwFac |
The bandwidth factor that gets passed on to
|
filterId |
A character used as filterId. |
plot |
Logical. Produce plots of filter results |
... |
Additional arguments. |
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
No preselection at all
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
.
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.
An ellipsoidGate
or list
of ellipsoidGate
objects
Class parameterFilter
,
directly.
Class concreteFilter
,
by class "parameterFilter", distance 2.
Class filter
, by class
"parameterFilter", distance 3.
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 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.
Florian Hahne
norm2Filter
,
curv1Filter
library(flowCore)
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.