arcTrans {flowSpecs} | R Documentation |
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".
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 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)