flowCore (version 1.38.2)

logTransform: 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.

See Also

transform-class, transform

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)