decoupler.mt.query_set

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decoupler.mt.query_set#

decoupler.mt.query_set(features, net, alternative='greater', n_bg=20000, ha_corr=0.5, tmin=5, verbose=False)#

Test overlap between a given feature set against a database of sets.

Parameters:

  • features (list) – Set of features

  • net (DataFrame) – Dataframe in long format. Must include source and target columns, and optionally a weight column.

  • alternative (str (default: 'greater')) – Defines the alternative hypothesis for fisher exact test. Check scipy.stats.fisher_exact.

  • n_bg (int | float | None (default: 20000)) – Number indicating the background size.

  • ha_corr (int | float (default: 0.5)) – Haldane-Anscombe correction of odds ratio.

  • tmin (int | float (default: 5)) – Minimum number of targets per source. Sources with fewer targets will be removed.

  • verbose (bool (default: False)) – Whether to display progress messages and additional execution details.

Returns:

Dataframe containing the odds ratio and fisher exact test p-values for the overlap of the given features across sets in a network.

Example

import decoupler as dc

ct = dc.op.collectri()
ft = set(ct[ct["source"] == "SMAD4"]["target"])
dc.mt.query_set(features=ft, net=ct)
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