Description Details Slots Objects from the Class Extends Note Author(s) References See Also Examples

Ratio transformation as parameterized in Gating-ML 2.0.

ratiotGml2 is defined by the following function:

*bound(f, boundMin, boundMax) =
max(min(f,boundMax),boundMin))*

where

*f(p1, p2, A, B, C) = A * (p1 - B) / (p2 - C)*

If a boundary is defined by the boundMin and/or boundMax parameters, then the result of this transformation is restricted to the [boundMin,boundMax] interval. Specifically, should the result of the f function be less than boundMin, then let the result of this transformation be boundMin. Analogically, should the result of the f function be more than boundMax, then let the result of this transformation be boundMax. The boundMin parameter shall not be greater than the boundMax parameter.

`.Data`

Object of class

`function`

.`numerator`

Object of class

`"transformation"`

– flow parameter to be used as numerator in the transformation function.`denominator`

Object of class

`"transformation"`

– flow parameter to be used as denominator in the transformation function.`pA`

Object of class

`numeric`

constant A.`pB`

Object of class

`numeric`

constant B.`pC`

Object of class

`numeric`

constant C.`transformationId`

Object of class

`"character"`

– unique ID to reference the transformation.`boundMin`

Object of class

`numeric`

– lower bound of the transformation, default -Inf.`boundMax`

Object of class

`numeric`

– upper bound of the transformation, default Inf.

Objects can be created by calls to the constructor

`ratiotGml2(p1, p2, A, B, C, transformationId, boundMin, boundMax)`

Class `"transform"`

, directly.

Class `"transformation"`

, by class "transform", distance 2.

Class `"characterOrTransformation"`

, by class "transform", distance 3.

The ratiotGml2 transformation object can be evaluated using the eval method by passing the data frame as an argument. The transformed parameters are returned as matrix with one column. (See example below)

Spidlen, J.

Gating-ML 2.0: International Society for Advancement of Cytometry (ISAC) standard for representing gating descriptions in flow cytometry. http://flowcyt.sourceforge.net/gating/20141009.pdf

`ratio`

, `transform-class`

,
`transform`

Other mathematical transform classes:
`EHtrans-class`

,
`asinht-class`

,
`asinhtGml2-class`

,
`dg1polynomial-class`

,
`exponential-class`

,
`hyperlog-class`

,
`hyperlogtGml2-class`

,
`invsplitscale-class`

,
`lintGml2-class`

,
`logarithm-class`

,
`logicletGml2-class`

,
`logtGml2-class`

,
`quadratic-class`

,
`ratio-class`

,
`sinht-class`

,
`splitscale-class`

,
`squareroot-class`

,
`unitytransform-class`

1 2 3 4 5 | ```
myDataIn <- read.FCS(system.file("extdata", "0877408774.B08",
package="flowCore"))
myRatioT <- ratiotGml2("FSC-H", "SSC-H", pA = 2, pB = 3,
pC = -10, transformationId = "myRatioT")
transOut <- eval(myRatioT)(exprs(myDataIn))
``` |

flowCore documentation built on Nov. 8, 2020, 5:19 p.m.

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