quadrantGate: Automated quad gating

In RGLab/flowStats: Statistical methods for the analysis of flow cytometry data

Automated quad gating

Description

This function tries to find the most likely separation of two-dimensional flow cytometry in four quadrants.

Usage

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)
						,...)

Arguments

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

Details

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.

Value

An object of class quadGate.

Author(s)

Florian Hahne

See Also

quadGate, rangeGate

Examples

## 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)

RGLab/flowStats documentation built on July 20, 2023, 1:33 a.m.