gate-class {prada} | R Documentation |
In flow-cytometry analysis, regions in two-dimensional projections of the data space often have to be selected. Objects of this class can store the properties of these selections.
Objects can be created using methods of the generic function
drawGate
or via
new("gate",
gateFun = ...., # function returning logical vector
colnames = .... # object of class character and length 2
logic = .... # object of class character
)
name
:gate
object. You can reference the object by its name for subsequent
operations (e.g. plotting).gateFun
:colnames
:logic
:character
object, either &
or
|
. This specifies the logical operation that will be applied
when combining the selection from the gate
with other object of
that class. See link[prada]{gateSet}
for additional information
on combining gates
.type
:character
giving the type of the
object. This is currently not used but might become important in the
future.boundaries
:matrix
with two columns
giving the boundaries of the gate in two dimensional space. Can be used
to superimpose the gate boundaries on a plot using lines()
.applyGate(x, data)
x
on data objects of class
cytoFrame
or matrix
.
In the former case x
may be of class gate
,
gateSet
, character
, numeric
or
logical
. See vignette for details.gate
object to gateSet
objectgate
objects to
one gateSet
objectFlorian Hahne
cytoFrame
, gateMatrix
,
gateSet
sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01", package="prada")) g1 <- new("gate", name="test1", gateFun=function(x)x[,"FSC-H"]<500, logic="&", colnames="FSC-H", type="misc") g1 g2 <- new("gate", name="test2", gateFun=function(x)x[,"SSC-H"]>800, logic="&", colnames="SSC-H", type="misc") gs1 <- combineGates(g1,g2) gs2 <- as.gateSet(g2) names(g1) names(g1) <- "testName" applyGate(sampdat, g1) applyGate(exprs(sampdat), g2) gate(sampdat) <- g1 applyGate(sampdat, 1) applyGate(sampdat, "testName") applyGate(sampdat, TRUE)