arcTrans {flowSpecs} | R Documentation

## Efficient inverse hyperbolic cosine transformation

### Description

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".

### Usage

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

### Arguments

`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!

### Value

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

### Examples

    # 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 check the data for the most optimal
    # transformation factors. For flow cytometry data, this can potentially be
    # done using the flowVS package:
    # https://www.bioconductor.org/packages/release/bioc/html/flowVS.html

    fullPanelTrans <- arcTrans(fullPanelUnmixed, transNames)

[Package flowSpecs version 1.1.2 Index]