def run_paired_t(bt, s1, s2):
'''Perform a paired t test between samples.
Parameters
----------
bt : biom table object
Table containing data for samples in s1 and s2.
s1 : list
List of sample ids found in bt (strs).
s2 : list
List of sample ids found in bt (strs).
Returns
-------
test_stats : list
Floats representing the test statistic for each paired comparison.
pvals : list
Floats representing the p-values of the reported test statistics.
'''
test_stats = []
pvals = []
s1_indices = [bt.index(i, axis='sample') for i in s1]
s2_indices = [bt.index(i, axis='sample') for i in s2]
for data in bt.iter_data(axis='observation'):
test_stat, pval = t_paired(data.take(s1_indices), data.take(s2_indices))
test_stats.append(test_stat)
pvals.append(pval)
return test_stats, pvals
def run_paired_t(bt, s1, s2):
'''Perform a paired t test between samples.
Parameters
----------
bt : biom table object
Table containing data for samples in s1 and s2.
s1 : list
List of sample ids found in bt (strs).
s2 : list
List of sample ids found in bt (strs).
Returns
-------
test_stats : list
Floats representing the test statistic for each paired comparison.
pvals : list
Floats representing the p-values of the reported test statistics.
'''
test_stats = []
pvals = []
s1_indices = [bt.index(i, axis='sample') for i in s1]
s2_indices = [bt.index(i, axis='sample') for i in s2]
for data in bt.iter_data(axis='observation'):
test_stat, pval = t_paired(data.take(s1_indices), data.take(s2_indices))
test_stats.append(test_stat)
pvals.append(pval)
return test_stats, pvals
def run_paired_t(data_generator):
"""Run paired t test on data."""
test_stats, pvals = [], []
for b_data, a_data in data_generator:
test_stat, pval = t_paired(b_data, a_data)
test_stats.append(test_stat)
pvals.append(pval)
return test_stats, pvals
def run_paired_t(data_generator):
"""Run paired t test on data."""
test_stats, pvals = [], []
for b_data, a_data in data_generator:
test_stat, pval = t_paired(b_data, a_data)
test_stats.append(test_stat)
pvals.append(pval)
return test_stats, pvals