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

Value

Returns an object of class transform.

Author(s)

B. Ellis and N. LeMeur

See Also

transform-class, transform

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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(flowCore)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowCore/lnTransform.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lnTransform
> ### Title: Create the definition of a ln transformation function (natural
> ###   logarthim) to be applied on a data set
> ### Aliases: lnTransform
> ### Keywords: methods
> 
> ### ** 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")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>