run.align: run.align - 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, using on of the CytofBatchAdjust functions

Usage

run.align()

Arguments

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.

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.align()

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