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# runAstir_cellstates

Source: `R/astir.R`
`runAstir_cellstates.Rd`

Predict cell states using Astir. This package requires the python library `astir` and `reticulate` to work. The function returns a `condor` object with automatically annotated cell states and QC of the annotation, the results are also saved in a folder specified by the user.

## Usage

    runAstir_cellstates(
      fcd,
      data_slot,
      analysis_path,
      manifest_name,
      max_epochs,
      learning_rate,
      initial_epochs,
      prefix = NULL
    )

## Arguments

fcd

  Flow cytometry dataset.

data_slot

  Data slot to use for the analysis (e.g. "orig" or "norm").

analysis_path

  Full path to the output folder of astir analysis.

manifest_name

  Filename of the manifest file, this file must be located in the `analysis_path` folder.

max_epochs

  Maximum number of epochs.

learning_rate

  Learning Rate.

initial_epochs

  Initial Epochs.

prefix

  Optional prefix for the slot name of the output.

## Value

runAstir_cellstates

## Details

Run Astir cell state prediction