View source: R/differential_expression.R

compare_expression | R Documentation |

Compare gene expression between two groups

```
compare_expression(
x,
umi,
group,
val1,
val2,
method = "LRT",
bin_size = 256,
cell_attr = x$cell_attr,
y = x$y,
min_cells = 5,
weighted = TRUE,
randomize = FALSE,
verbosity = 2,
verbose = NULL,
show_progress = NULL
)
```

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

`umi` |
A matrix of UMI counts with genes as rows and cells as columns |

`group` |
A vector indicating the groups |

`val1` |
A vector indicating the values of the group vector to treat as group 1 |

`val2` |
A vector indicating the values of the group vector to treat as group 2 |

`method` |
Either 'LRT' for likelihood ratio test, or 't_test' for t-test |

`bin_size` |
Number of genes that are processed between updates of progress bar |

`cell_attr` |
Data frame of cell meta data |

`y` |
Only used if methtod = 't_test', this is the residual matrix; default is x$y |

`min_cells` |
A gene has to be detected in at least this many cells in at least one of the groups being compared to be tested |

`weighted` |
Balance the groups by using the appropriate weights |

`randomize` |
Boolean indicating whether to shuffle group labels - only set to TRUE when testing methods |

`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 |

Data frame of results

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