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# harmonize_intensities

Source: `R/batch_correction.R`
`harmonize_intensities.Rd`

Harmonize the expression values for a defined batch variable (`batch_var`).

## Usage

    harmonize_intensities(fcd, batch_var, seed = 91)

## Arguments

fcd

  flow cytometry dataset.

batch_var

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

seed

  A seed is set for reproducibility.

## Value

The function returns a fcd with a harmonized expression data frame based on `HarmonyMatrix`. The harmonized expression data frame is saved in `fcd$expr$norm`.

## Details

harmonize_intensities

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