run.align - Run the alignment model on a target data.table

This function allows you to prepare reference data ahead of performing batch alignment, using on of the CytofBatchAdjust functions

Usage

run.align()

ref.dat: NO DEFAULT. A data.table consisting of the 'refernece' data you will use to train the alignment algorithm
target.dat: NO DEFAULT.A data.table consisting of the 'target' data you will use to align the data
batch.col: NO DEFAULT. Column name of the data.table that contains batch labels
align.cols: NO DEFAULT. Vector of column names to align.
method: DEFAULT = 'quantile'. Can be 'quantile', 'SD', or a percentile indicated as '50p' (50th percentile) or '95p' (95th percentile) etc.
append.name: DEFAULT = "_aligned". This will be appended to the column names containing the aligned data
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.

Returns a data.table with aligned data added in new columns.