calour.analysis.diff_abundance_kw¶

calour.analysis.diff_abundance_kw(exp: calour.experiment.Experiment, field, transform='rankdata', numperm=1000, alpha=0.1, fdr_method='dsfdr', random_seed=None)[source]¶

Test the differential expression between multiple sample groups using the Kruskal Wallis test. uses a permutation based fdr (dsfdr) for bacteria that have a significant difference.

Note

This function is also available as a class method Experiment.diff_abundance_kw()

Parameters:	exp (Experiment) – Input experiment object. exp – field (str) – The field to test by transform (str or None) – transformation to apply to the data before caluculating the statistic ‘rankdata’ : rank transfrom each OTU reads ‘log2data’ : calculate log2 for each OTU using minimal cutoff of 2 ‘normdata’ : normalize the data to constant sum per samples ‘binarydata’ : convert to binary absence/presence alpha (float) – the desired FDR control level numperm (int) – number of permutations to perform random_seed (int or None (optional)) – int to set the numpy random seed to this number before running the random permutation test. None to not set the numpy random seed
Returns:	newexp – The experiment with only significant (FDR<=maxfval) difference, sorted according to difference
Return type:	Experiment