lnTransform: Create the definition of a ln transformation function...

In RGLab/flowCore: flowCore: Basic structures for flow cytometry data

Create the definition of a ln transformation function (natural logarthim) to be applied on a data set

Description

Create the definition of the ln Transformation that will be applied on some parameter via the transform method. The definition of this function is currently x<-log(x)*(r/d). The transformation would normally be used to convert to a linear valued parameter to the natural logarithm scale. Typically r and d are both equal to 1.0. Both must be positive.

Usage

lnTransform(transformationId="defaultLnTransform", r=1, d=1)

Arguments

transformationId	character string to identify the transformation
r	positive double that corresponds to a scale factor.
d	positive double that corresponds to a scale factor

Value

Returns an object of class transform.

Author(s)

B. Ellis and N. LeMeur

See Also

transform-class, transform

Other Transform functions: arcsinhTransform(), biexponentialTransform(), inverseLogicleTransform(), linearTransform(), logTransform(), logicleTransform(), quadraticTransform(), scaleTransform(), splitScaleTransform(), truncateTransform()

Examples

  data(GvHD)
  lnTrans <- lnTransform(transformationId="ln-transformation", r=1, d=1)
  ln1 <- transform(GvHD, transformList('FSC-H', lnTrans))

opar = par(mfcol=c(2, 1))
plot(density(exprs(GvHD[[1]])[ ,1]), main="Original")
plot(density(exprs(ln1[[1]])[ ,1]), main="Ln Transform")

RGLab/flowCore documentation built on Aug. 26, 2024, 8:52 a.m.