grassp.tl.mr_score

mr_score(data, condition_key, replicate_key, mcd_proportion=0.75, assume_centered=True, n_iterations=11, key_added='mr_scores')

M/R score for detecting protein translocation.

Implements the approach from Itzhak et al. 2016 where M is a moderated t-statistic (via Minimum Covariance Determinant) and R the measure of reproducibility between replicates.

Parameters:

data AnnData

AnnData object containing all conditions/replicates stacked in variables.

condition_key str

Observation column indicating the experimental condition (e.g. control, treatment).

replicate_key str

Column indicating biological replicates.

mcd_proportion float (default: 0.75)

Parameters forwarded to sklearn.covariance.MinCovDet().

assume_centered bool (default: True)

Parameters forwarded to sklearn.covariance.MinCovDet().

n_iterations int (default: 11)

Parameters forwarded to sklearn.covariance.MinCovDet().

key_added str (default: 'mr_scores')

Base name for the two new columns {key_added}_M and {key_added}_R written to data.obs.

Return type:

None