quadrantGate {flowStats} | R Documentation |
This function tries to find the most likely separation of two-dimensional flow cytometry in four quadrants.
quadrantGate(x, stains, alpha=c("min", "min"), sd=c(2, 2), plot=FALSE, filterId="defaultQuadGate", ...)
x |
A flowSet or
flowFrame . |
stains |
A character vector of length two giving the two flow parameters for which the quad gate is to be computed. |
alpha, sd |
Tuning factors to control the computation of the
gate boundaries. See rangeGate for details. |
plot |
Logical. Produce plots of intermediate results. |
filterId |
Character, the name assigned to the resulting filter. |
... |
Additional arguments |
The most likely separation between postitive and negative stains for
two-dimensional data is computed based on density
estimates. Essentially, the gate parameters are first fitted
separately for the two parameters and later combined. See the
documentation for rangeGate
for details. There is a
certain amount of heuristics involved in this process. The algorithm
can be slightly tweaked using the alpha
and sd
arguments. Their values will be recycled for the two dimensions unless
explicitely given as vectors of length 2.
An object of class quadGate
.
Florian Hahne
data(GvHD) dat <- GvHD[pData(GvHD)$Patient==10] dat <- transform(dat, "FL4-H"=asinh(`FL4-H`), "FL2-H"=asinh(`FL2-H`)) qg <- quadrantGate(dat, c("FL2-H", "FL4-H")) qg if(require(flowViz)) xyplot(`FL2-H`~`FL4-H`, dat, filter=qg) qg <- quadrantGate(dat, c("FL2-H", "FL4-H"), alpha=c(0.1, 0.9), plot=TRUE)