gatac.tl.get_marker_peaks

gatac.tl.get_marker_peaks(adata, key='marker_peaks', group=None, fdr_threshold=0.05, log2_fc_threshold=0.0, n_peaks=None)

Extract marker peak names from stored results.

Convenience function to get peak names passing significance thresholds.

Parameters:

adata AnnData

Annotated data with marker peak results in uns.

key str

Key in adata.uns containing results from marker_peaks.

group str, optional

Specific group to extract. If None, return all groups.

fdr_threshold float

FDR threshold (default: 0.05).

log2_fc_threshold float

Minimum absolute log2 fold change (default: 0.0).

n_peaks int, optional

Maximum number of peaks per group.

Returns:

dict or list Dictionary mapping group names to peak lists, or list if group specified.

Return type:

dict[str, list[str]] | list[str]

Examples

>>> import gatac as ga
>>> # All groups at once
>>> markers_by_group = ga.tl.get_marker_peaks(adata, fdr_threshold=0.05)
>>> # A single group's top peaks
>>> top_peak_names = ga.tl.get_marker_peaks(adata, group="CD8_T", fdr_threshold=0.05, n_peaks=100)