ratiotGml2-class {flowCore} | R Documentation |
Ratio 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(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.
Objects can be created by calls to the constructor
ratiotGml2(p1, p2, A, B, C, transformationId, boundMin, boundMax)
.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
Class "transform"
, directly.
Class "transformation"
, by class "transform", distance 2.
Class "characterOrTransformation"
, by class "transform", distance 3.
No methods defined with class "ratiotGml2" in the signature.
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
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))