batchNormCtrlSetup: Setup the file used for batch normalisation

In jtheorell/theFlowSpec: Tools for spectral unmixing of overdetermined flow-cytometry files. And other nice things.

Description

This function is used to generate the batch normalization values that ideally are based on an identical control that is included in each experiment.

Usage

batchNormCtrlSetup(ctrlFrame, normNames = colnames(ctrlFrame),
  exclColNmStr = c("ime"), volThresh = 0.05, lowVertThresh = 0.25,
  transCoFacs = "default", nonLevel1Var)

Arguments

ctrlFrame	A control flowFrame that all the batches will be normalized to.
normNames	The variables that should be normalized. Default is all that do not fall into one of the two excl categories below.
exclColNmStr	A vector of strings that are not accepted in any normNames.
volThresh	Defining how small the smaller of the two peaks can be to be considered a true peak. It is a fraction of the volume of the larger peak. Default is 0.05, i.e. if the volume of the second peak is 5 percent or larger than the volume of the first peak, it is considered a peak.
lowVertThresh	Defining how low the turnpoint needs to be between the peaks for these to be considered well-separated. 25 percent of the lower peak is the default.
transCoFacs	This vector of named values define the values for the transformation during the normalization. This is only applied internally, so transformation needs to be performed afterwards, preferrably with individual values for each channel. In the "default" case, the function defines the file as a CyTOF file, and applies the transformation value 8, if >5 percent of the values are 0. Otherwise, the value 256 is applied. NB. The entries need to be named in the same way as the normNames to secure that the right factor is added to each variable.
nonLevel1Var	If any of the markers are known to be unreliable, these will be excluded from being used as filters for other markers.

jtheorell/theFlowSpec documentation built on Aug. 22, 2019, 3:33 a.m.