arcTrans: Efficient inverse hyperbolic cosine transformation
In flowSpecs: Tools for processing of high-dimensional cytometry data

Description Usage Arguments Value Examples

This is a simple wrapper function for the base asinh function, that is useful for flowFrames and flowSets. It also allows for reversing the transformation with the argument "unTrans".

1	arcTrans(flowObj, transNames, transCoFacs = "default", unTrans = FALSE)

`flowObj`	The fcs object to be transformed. Both flowFrames and flowSets are accepted.
`transNames`	The variables that should be normalized.
`transCoFacs`	This value or vector of values define the values for the transformation during the normalization. In the "default" case, the function defines the object as a CyTOF object if >5 percent of the values are 0, and applies the transformation value 5. Otherwise, the value 400 is applied.
`unTrans`	If the reverse action should be taken, i.e. if an already transformed dataset should be un-transformed. NB! It is of great importance that the same transformation factors are used!

A flow object containing the transformed data, and with all metadata left untouched.

# Import some data and the spectral matrix. The latter can be generated using
# specMatCalc
data(fullPanel)
data(specMat)

fullPanelUnmixed <- specUnmix(fullPanel, specMat)

# Identify the columns that should be transformed
colnames(fullPanelUnmixed)
# The time and scatter parameters should not, but apart from that, all should
# be included.
transNames <- colnames(fullPanelUnmixed)[seq(6,18)]

# ow, transform this file, with the default transformation factor of 400.
# NB! It is alway advisable to visually (or computationally) check the data
# for the most optimal transformation factors. These often vary from marker
# to marker.

fullPanelTrans <- arcTrans(fullPanelUnmixed, transNames)