gateSet-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 for several of these selections
Objects can be created using methods of the generic function
drawGate
or via
new("gateSet",
glist = ...., # object of class list
)
name
:character
giving the name
of the object. You can reference the object by its name for subsequent
operations (e.g. plotting).glist
:"list"
with items of
class gate
. The individual
gate
objects will be combined according to
the value of their slot logic
.applyGate(x, data)
x
on data objects of class
cytoFrame
or matrix
.glist
.display summary
gate
objects.gateSet
objects. gate
objects. gate
or gateSet
to a
cytoFrame
Florian Hahne
sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01", package="prada")) g1 <- new("gate", name="G1", gateFun=function(x)x[,"FSC-H"]<500, logic="&", colnames="FSC-H") g2 <- new("gate", name="G2", gateFun=function(x)x[,"SSC-H"]>800, logic="&", colnames="SSC-H") g3 <- new("gate", name="G3", gateFun=function(x)x[,"FL1-H"]>800, logic="&", colnames="FL1-H") gs <- new("gateSet", name="Set1", glist=list(G1=g1, G2=g2)) length(gs) gs[[1]] gs[1] gsnames <- names(gs) names(gs) <- gsnames applyGate(sampdat, gs) applyGate(exprs(sampdat), gs) gate(sampdat) <- gs applyGate(sampdat, 1) applyGate(sampdat, "G1") applyGate(sampdat, TRUE) appendGates(sampdat, g3)