Hi,
I am using the HINT differential analysis module with Atac-seq data. It is working great, but I am wondering how are the p-values adjusted ? I found this function in DifferentialAnalysis.py
def adjust_p_values(p_values): p = np.asfarray(p_values) by_descend = p.argsort()[::-1] by_orig = by_descend.argsort() steps = float(len(p)) / np.arange(len(p), 0, -1) q = np.minimum(1, np.minimum.accumulate(steps * p[by_descend])) return q[by_orig]
which is apparently applying Benjamini-Hochberg correction, but the function is not called anywhere in the script ? Are the p-values corrected then ?
Thank you in advance.
Best regards,
Romain
Hi,
I am using the HINT differential analysis module with Atac-seq data. It is working great, but I am wondering how are the p-values adjusted ? I found this function in DifferentialAnalysis.py
def adjust_p_values(p_values): p = np.asfarray(p_values) by_descend = p.argsort()[::-1] by_orig = by_descend.argsort() steps = float(len(p)) / np.arange(len(p), 0, -1) q = np.minimum(1, np.minimum.accumulate(steps * p[by_descend])) return q[by_orig]which is apparently applying Benjamini-Hochberg correction, but the function is not called anywhere in the script ? Are the p-values corrected then ?
Thank you in advance.
Best regards,
Romain