quadrantGate: Automated quad gating
In flowStats: Statistical methods for the analysis of flow cytometry data

Description Usage Arguments Details Value Author(s) See Also Examples

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", refLine.1=NULL, refLine.2=NULL
				 		,rare=c(FALSE,FALSE)
				 		,sig=c(NULL,NULL)
						,...)

`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.
`refLine.1`	Either `NULL` or a numeric of lenth 1. If `NULL`, this parameter is ignored. When it is set to a numeric, the minor sub-population (if any) below this reference line in the first stain channel will be igored while determining the separator between positive and negative.
`refLine.2`	Either `NULL` or a numeric of lenth 1. If `NULL`, this parameter is ignored. When it is set to a numeric, the minor sub-population (if any) below this reference line in the second stain channel will be igored while determining the separator between positive and negative.
`rare`	logical flags for two channels, Refer to `density1d` for more details.
`sig`	parameters for two channels. Refer to `density1d` for more details.
`...`	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

quadGate, rangeGate

## Not run: 
library(flowCore)
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)
qg
split(dat, qg)

## End(Not run)