cell2clone.permutation_test

cell2clone.permutation_test(df, reference_celltype, value_col='clone_size_score', celltype_col='cell_type', sample_col='sample_id', percentile=0.99, n_perms=10000, min_samples=10, random_state=0)

Test whether a cell type contains more highly clonal samples than a reference cell type.

The threshold is defined from a percentile of the reference cell type, and significance is assessed by permutation of cell-type labels.

Parameters

dfpandas.DataFrame

Sample-level clonality metrics.

reference_celltypestr

Cell type used to define the threshold.

…

Returns

pandas.DataFrame

Permutation test results with raw and FDR-adjusted p-values.