quadrantGate {flowStats} | R Documentation

## 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)

[Package flowStats version 4.0.0 Index]