init#

DE.__init__(source=None, /, *, table, voom_weights=None, voom_plot_data=None)[source]#

Initialize the DE object.

Parameters:

source : str | Path | None
a directory containing a DE object saved with save(). Mutually exclusive with table, voom_weights, and voom_plot_data.
table : DataFrame
a polars DataFrame containing the DE results, with columns:
- cell_type: the cell type in which DE was tested
- coefficient: the coefficient (or contrast) for which DE
  was tested
- gene: the gene for which DE was tested
- logFC: the log2 fold change of the gene, i.e. its effect
  size
- SE: the standard error of the effect size
- LCI: the lower 95% confidence interval of the effect size
- UCI: the upper 95% confidence interval of the effect size
- AveExpr: the gene’s average expression in this cell type,
  in log CPM
- p: the DE p-value
- Bonferroni: the Bonferroni-corrected DE p-value
- FDR: the FDR q-value for the DE
Mutually exclusive with source.
voom_weights : dict[str, DataFrame] | None
an optional {cell_type: DataFrame} dictionary of voom weights, where rows are genes and columns are samples. The first column of each cell type’s DataFrame, ‘gene’, contains the gene names. Mutually exclusive with source.
voom_plot_data : dict[str, DataFrame] | None
an optional {cell_type: DataFrame} dictionary of info necessary to construct a voom plot with DE.plot_voom(). Mutually exclusive with source.

Return type:

None

__init__#