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.