lymphFilter-class {flowStats} | 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", evaluate=TRUE, 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. |
evaluate |
A logical indicating wether the filter should be
resolved (computation of the
|
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.
A list with items
x |
The filtered |
n2gate |
The |
n2gateResults |
The
|
for the lymphGate
function. Note that x
and
n2gateResults
are NULL
when eval=FALSE
.
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
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)