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
def run_single_paired_T_test(OTU, mapping_data, header, individual_column,\
timepoint_zero_column, otu_table, ignore_val, filt):
"""run the paired T test on a single OTU
"""
timepoint_zero_vals, after_treatment_vals = get_single_paired_T_values(OTU,
mapping_data, header, individual_column, timepoint_zero_column,
otu_table, ignore_val)
#get the number of samples from the category mapping and multiply by the filter
#two samples per individual so divide by 2
filt = (filt*len(mapping_data))/2
if len(timepoint_zero_vals) >= round(filt):
t, prob = t_paired(timepoint_zero_vals, after_treatment_vals,
tails=None, exp_diff=0)
return t, prob, after_treatment_vals, len(after_treatment_vals)
else:
return None
def run_single_paired_T_test(OTU, mapping_data, header, individual_column,\
timepoint_zero_column, otu_table, ignore_val, filt):
"""run the paired T test on a single OTU
"""
timepoint_zero_vals, after_treatment_vals = get_single_paired_T_values(
OTU, mapping_data, header, individual_column, timepoint_zero_column,
otu_table, ignore_val)
#get the number of samples from the category mapping and multiply by the filter
#two samples per individual so divide by 2
filt = (filt * len(mapping_data)) / 2
if len(timepoint_zero_vals) >= round(filt):
t, prob = t_paired(timepoint_zero_vals,
after_treatment_vals,
tails=None,
exp_diff=0)
return t, prob, after_treatment_vals, len(after_treatment_vals)
else:
return None
