logTransform: Create the definition of a log transformation function (base...

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

Create the definition of a log transformation function (base specified by user) to be applied on a data set

Description

Create the definition of the log Transformation that will be applied on some parameter via the transform method. The definition of this function is currently x<-log(x,logbase)*(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. logbase = 10 corresponds to base 10 logarithm.

Usage

logTransform(transformationId="defaultLogTransform", logbase=10, r=1, d=1)

Arguments

transformationId	character string to identify the transformation
logbase	positive double that corresponds to the base of the logarithm.
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, N. LeMeur

See Also

transform-class, transform

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

Examples

samp <- read.FCS(system.file("extdata",
   "0877408774.B08", package="flowCore"))
  logTrans <- logTransform(transformationId="log10-transformation", logbase=10, r=1, d=1)
  trans <- transformList('FSC-H', logTrans)
  dataTransform <- transform(samp, trans)

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