correct | R Documentation |

Correct data by setting all latent factors to their median values and reversing the regression model

correct( x, data = "y", cell_attr = x$cell_attr, as_is = FALSE, do_round = TRUE, do_pos = TRUE, scale_factor = NA, verbosity = 2, verbose = NULL, show_progress = NULL )

`x` |
A list that provides model parameters and optionally meta data; use output of vst function |

`data` |
The name of the entry in x that holds the data |

`cell_attr` |
Provide cell meta data holding latent data info |

`as_is` |
Use cell attributes as is and do not use the median; set to TRUE if you want to manually control the values of the latent factors; default is FALSE |

`do_round` |
Round the result to integers |

`do_pos` |
Set negative values in the result to zero |

`scale_factor` |
Replace all values of UMI in the regression model by this value. Default is NA which uses median of total UMI as the latent factor. |

`verbosity` |
An integer specifying whether to show only messages (1), messages and progress bars (2) or nothing (0) while the function is running; default is 2 |

`verbose` |
Deprecated; use verbosity instead |

`show_progress` |
Deprecated; use verbosity instead |

Corrected data as UMI counts

vst_out <- vst(pbmc, return_cell_attr = TRUE) umi_corrected <- correct(vst_out)

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