# Class asinhtGml2

### Description

Inverse hyperbolic sin transformation as parameterized in Gating-ML 2.0 is defined by the following function:

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

where

*f(parameter, T, M, A) = (asinh(parameter * sinh(M * ln(10)) / T) +A * ln(10)) / ((M + A) * ln(10))*

This transformation is equivalent to Logicle(T, 0, M, A) (i.e., with W=0). It provides an inverse hyperbolic sine transformation that maps a data value onto the interval [0,1] such that:

The top of scale value (i.e., T ) is mapped to 1.

Large data values are mapped to locations similar to an (M + A)-decade logarithmic scale.

A decades of negative data are brought on scale.

In addition, 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.

### Objects from the Class

Objects can be created by calls to the constructor

`asinhtGml2(parameter, T, M, A, transformationId, boundMin, boundMax)`

### Slots

`.Data`

:Object of class

`function`

~~`T`

:Object of class

`numeric`

-positive constant (top of scale value)`M`

:Object of class

`numeric`

-positive constant (desired number of decades)`A`

:Object of class

`numeric`

-non-negative constant that is less than or equal to M (desired number of additional negative decades)`parameters`

:Object of class

`"transformation"`

-flow parameter to be transformed`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

### Extends

Class `singleParameterTransform`

, directly.
Class `transform`

, by class singleParameterTransform, distance 2.
Class `transformation`

, by class singleParameterTransform, distance 3.
Class `characterOrTransformation`

, by class singleParameterTransform, distance 4.

### Methods

No methods defined with class asinhtGml2 in the signature.

### Note

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

### Author(s)

Spidlen, J.

### References

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

### See Also

`asinht`

, `transform-class`

, `transform`

### Examples

1 2 3 4 5 | ```
myDataIn <- read.FCS(system.file("extdata", "0877408774.B08",
package="flowCore"))
myASinH1 <- asinhtGml2(parameters = "FSC-H", T = 1000, M = 4.5,
A = 0, transformationId="myASinH1")
transOut <- eval(myASinH1)(exprs(myDataIn))
``` |