train.cytonorm - Prepare reference data into a FlowSOM object

This function allows you to learn the conversions to use for batch alignment.

Usage

train.align()

method: DEFAULT = 'cytonorm'. In future additional methods for batch alignment will be added.
cytonorm.goal: DEFAULT = 'mean'. Target values for alignment. Can be 'mean' for the average of all batches, or a specific batch can be selected.
cytonorm.nQ: DEFAULT = 101. Number of quantiles.
dir: DEFAULT = getwd(). Sets the working directory to operate from. Because this function involves some reading/writing of files, it's best to set this to somewhere static in case the active working directory moves to a subfolder, and then doesn't return because the function runs into an error.
mem.ctrl: DEFAULT = TRUE. Allows the function to clear held memory on occasion.
dat: NO DEFAULT. A data.table consisting of the 'refernece' data you will use to train the alignment algorithm
cellular.cols: NO DEFAULT. A vector of column names from the data.table that contain the markers to be aligned

Returns the alignment model object, with an additional 'conversions' element added.