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harmonize_PCA

Source: R/batch_correction.R
harmonize_PCA.Rd

Harmonize the Principal Components previously calculated by runPCA for a defined batch variable (batch_var).

Usage

harmonize_PCA(fcd, data_slot = "orig", batch_var, seed = 91, prefix = NULL)

Arguments

fcd

flow cytometry dataset.

data_slot

name of the PCA data slot to use for harmonization. If no prefix was added the, orig.

batch_var

vector of column names from fcd$anno$cell_anno to use for correcting the data.

seed

A seed is set for reproducibility.

prefix

Prefix for the output.

Value

The function returns a fcd with a harmonized Principal Components based on HarmonyMatrix. If no prefix is added, the harmonized PCs are saved in fcd$pca$norm.

Details

harmonize_PCA

See [Korunsky et al., 2019](https://doi.org/10.1038/s41592-019-0619-0) for more details on the Harmony algorithm.