spateo.tools.cci_fdr

Companion functions for cell-cell communication inference analyses

Functions

fdr_correct(→ pandas.DataFrame)

Correct p-values for FDR along specific axis in pvals.

Module Contents

spateo.tools.cci_fdr.fdr_correct(pvals: pandas.DataFrame, corr_method: str, corr_axis: Literal['interactions', 'clusters'] = 'clusters', alpha: float = 0.05) → pandas.DataFrame

Correct p-values for FDR along specific axis in pvals.

Parameters:

pvals

pd.DataFrame

corr_method

str Correction method, should be one of the options in :func statsmodels.stats.multitest.multipletests (listed below for reference):

• Named methods:

  • bonferroni

  • sidak

  • holm-sidak

  • holm

  • simes-hochberg

  • hommel

• Abbreviated methods:

  • fdr_bh: Benjamini-Hochberg correction

  • fdr_by: Benjamini-Yekutieli correction

  • fdr_tsbh: Two-stage Benjamini-Hochberg

  • fdr_tsbky: Two-stage Benjamini-Krieger-Yekutieli method

corr_axis

str Either “interactions” or “clusters”- specifies whether the dataframe given to ‘pvals’ corresponds to samples or interactions. If ‘interactions’, will need to transpose the array first before performing multiple hypothesis correction.