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Add W rank sum statistic to hicDifferentialTAD outpu #728

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merged 2 commits into from
Jun 30, 2021
Merged

Add W rank sum statistic to hicDifferentialTAD outpu #728

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864e947
Output Ranksum statistics
dawe Jun 22, 2021
92e0d86
fix a bug that prevented stats to be printed
dawe Jun 23, 2021
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31 changes: 27 additions & 4 deletions hicexplorer/hicDifferentialTAD.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,7 @@ def computeDifferentialTADs(pMatrixTarget, pMatrixControl, pDomainList, pCoolOrH
accepted_inter_right = []
accepted_intra = []
p_values_list = []
stats_list = []
rows = []

old_chromosome = None
Expand Down Expand Up @@ -241,45 +242,56 @@ def computeDifferentialTADs(pMatrixTarget, pMatrixControl, pDomainList, pCoolOrH
log.debug('left statistic {}, significance_level {}'.format(statistic_left, significance_level_left))

p_values = []
stats = []
if significance_level_left is None or np.isnan(significance_level_left):
accepted_inter_left.append(0)
p_values.append(np.nan)
stats.append(np.nan)
elif significance_level_left <= pPValue:
accepted_inter_left.append(1)
p_values.append(significance_level_left)
stats.append(statistic_left)
else:
accepted_inter_left.append(0)
p_values.append(significance_level_left)
stats.append(statistic_left)

if significance_level_right is None or np.isnan(significance_level_right):
accepted_inter_right.append(0)
p_values.append(np.nan)
stats.append(np.nan)
elif significance_level_right <= pPValue:
accepted_inter_right.append(1)
p_values.append(significance_level_right)
stats.append(statistic_right)
else:
accepted_inter_right.append(0)
p_values.append(significance_level_right)
stats.append(statistic_right)

if significance_level is None or np.isnan(significance_level):
accepted_intra.append(0)
p_values.append(np.nan)
stats.append(np.nan)
elif significance_level <= pPValue:
accepted_intra.append(1)
p_values.append(significance_level)
stats.append(statistic)
else:
accepted_intra.append(0)
p_values.append(significance_level)
stats.append(statistic)

p_values_list.append(p_values)
stats_list.append(stats)

rows.append(row)
except Exception as exp:
pQueue.put('Fail: ' + str(exp) + traceback.format_exc())
return
# hic_matrix_target_inter_tad.save('manipulated_target.cool')
# hic_matrix_control_inter_tad.save('manipulated_control.cool')
pQueue.put([p_values_list, accepted_inter_left, accepted_inter_right, accepted_intra, rows])
pQueue.put([stats_list, p_values_list, accepted_inter_left, accepted_inter_right, accepted_intra, rows])


def main(args=None):
Expand All @@ -305,6 +317,7 @@ def main(args=None):
# log.debug('domains_df {}'.format(domains_df))
domains = domains_df.values.tolist()

stats_threads = [None] * args.threads
p_values_threads = [None] * args.threads
accepted_left_inter_threads = [None] * args.threads
accepted_right_inter_threads = [None] * args.threads
Expand Down Expand Up @@ -360,7 +373,7 @@ def main(args=None):
fail_flag = True
fail_message = queue_data
else:
p_values_threads[i], accepted_left_inter_threads[i], \
stats_threads[i], p_values_threads[i], accepted_left_inter_threads[i], \
accepted_right_inter_threads[i], \
accepted_intra_threads[i], rows_threads[i] = queue_data

Expand All @@ -382,12 +395,14 @@ def main(args=None):
log.error(fail_message[6:])
exit(1)

stats_list = [item for sublist in stats_threads for item in sublist]
p_values_list = [item for sublist in p_values_threads for item in sublist]
accepted_inter_left = [item for sublist in accepted_left_inter_threads for item in sublist]
accepted_inter_right = [item for sublist in accepted_right_inter_threads for item in sublist]
accepted_intra = [item for sublist in accepted_intra_threads for item in sublist]
rows = [item for sublist in rows_threads for item in sublist]

stats_list = np.array(stats_list)
p_values_list = np.array(p_values_list)
accepted_inter_left = np.array(accepted_inter_left)
accepted_inter_right = np.array(accepted_inter_right)
Expand Down Expand Up @@ -417,28 +432,33 @@ def main(args=None):
mask = np.logical_or(mask, accepted_intra)

accepted_H0 = p_values_list[~mask]
accepted_H0_s = stats_list[~mask]
rejected_H0 = p_values_list[mask]
rejected_H0_s = stats_list[mask]
accepted_rows = rows[~mask]
rejected_rows = rows[mask]
with open(args.outFileNamePrefix + '_accepted.diff_tad', 'w') as file:
header = '# Created with HiCExplorer\'s hicDifferentialTAD version ' + __version__ + '\n'
header += '# H0 \'regions are equal\' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential.\n'
header += '# Accepted regions with Wilcoxon rank-sum test to p-value: {} with used mode: {} and modeReject: {} \n'.format(args.pValue, args.mode, args.modeReject)
header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n'
header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\tW left-inter-TAD\tW right-inter-TAD\tW intra-TAD\n'
file.write(header)
for i, row in enumerate(accepted_rows):
row_list = list(map(str, row))
file.write('\t'.join(row_list))
file.write('\t')
pvalue_list = list(map(str, accepted_H0[i]))
file.write('\t'.join(pvalue_list))
file.write('\t')
stats_list = list(map(str, accepted_H0_s[i]))
file.write('\t'.join(stats_list))

file.write('\n')
with open(args.outFileNamePrefix + '_rejected.diff_tad', 'w') as file:
header = '# Created with HiCExplorer\'s hicDifferentialTAD version ' + __version__ + '\n'
header += '# H0 \'regions are equal\' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.\n'
header += '# Rejected regions with Wilcoxon rank-sum test to p-value: {} with used mode: {} and modeReject: {} \n'.format(args.pValue, args.mode, args.modeReject)
header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n'
header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\tW left-inter-TAD\tW right-inter-TAD\tW intra-TAD\n'

file.write(header)

Expand All @@ -448,4 +468,7 @@ def main(args=None):
file.write('\t')
pvalue_list = list(map(str, rejected_H0[i]))
file.write('\t'.join(pvalue_list))
file.write('\t')
stats_list = list(map(str, rejected_H0_s[i]))
file.write('\t'.join(stats_list))
file.write('\n')