flowCore (version 1.38.2)

lnTransform: 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.

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")