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

In flowCore: flowCore: Basic structures for flow cytometry data

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)

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