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

In sydneycytometry/Spectre: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data.

Description

This function allows you to prepare reference data ahead of performing batch alignment.

Usage

run.align()

Arguments

dat	NO DEFAULT. A data.table consisting of the 'refernece' data you will use to train the alignment algorithm
model	NO DEFAULT. A batch alignment conversion model object created by the prep.align() and train.align() functions.
batch.col	NO DEFAULT. Column name of the data.table that contains batch labels
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.

Value

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

Author(s)

Thomas M Ashhurst, [e-mail]

References

Ashhurst, T. M., et al. (2019). https://www.ncbi.nlm.nih.gov/pubmed/31077106

Examples

cell.dat <- run.cytonorm()

sydneycytometry/Spectre documentation built on March 20, 2021, 2:15 a.m.