gseapy/stats.py
def fdrcorrection(pvals, alpha=0.05):
    """ benjamini hocheberg fdr correction. inspired by statsmodels 
    """
    # Implement copy from GOATools.
    pvals = np.asarray(pvals)
    pvals_sortind = np.argsort(pvals)
    pvals_sorted = np.take(pvals, pvals_sortind)

    ecdffactor = _ecdf(pvals_sorted)
    reject = pvals_sorted <= ecdffactor*alpha
    if reject.any():
        rejectmax = max(np.nonzero(reject)[0])
        reject[:rejectmax] = True
    pvals_corrected_raw = pvals_sorted / ecdffactor
    pvals_corrected = np.minimum.accumulate(pvals_corrected_raw[::-1])[::-1]
    del pvals_corrected_raw
    pvals_corrected[pvals_corrected>1] = 1
    pvals_corrected_ = np.empty_like(pvals_corrected)
    pvals_corrected_[pvals_sortind] = pvals_corrected
    del pvals_corrected
    reject_ = np.empty_like(reject)
    reject_[pvals_sortind] = reject
    return reject_, pvals_corrected_
def fdrcorrection(pvals, alpha=0.05):
    # Implement copy from GOATools.
    pvals = np.asarray(pvals)
    pvals_sortind = np.argsort(pvals)
    pvals_sorted = np.take(pvals, pvals_sortind)

    ecdffactor = _ecdf(pvals_sorted)
    reject = pvals_sorted <= ecdffactor*alpha
    if reject.any():
        rejectmax = max(np.nonzero(reject)[0])
        reject[:rejectmax] = True
    pvals_corrected_raw = pvals_sorted / ecdffactor
    pvals_corrected = np.minimum.accumulate(pvals_corrected_raw[::-1])[::-1]
    del pvals_corrected_raw
    pvals_corrected[pvals_corrected>1] = 1
    pvals_corrected_ = np.empty_like(pvals_corrected)
    pvals_corrected_[pvals_sortind] = pvals_corrected
    del pvals_corrected
    reject_ = np.empty_like(reject)
    reject_[pvals_sortind] = reject
    return reject_, pvals_corrected_
def fdrcorrection ( pvals , alpha = 0.05 ) : # Implement copy from GOATools. pvals = np . asarray ( pvals ) pvals_sortind = np . argsort ( pvals ) pvals_sorted = np . take ( pvals , pvals_sortind ) ecdffactor = _ecdf ( pvals_sorted ) reject = pvals_sorted <= ecdffactor * alpha if reject . any ( ) : rejectmax = max ( np . nonzero ( reject ) [ 0 ] ) reject [ : rejectmax ] = True pvals_corrected_raw = pvals_sorted / ecdffactor pvals_corrected = np . minimum . accumulate ( pvals_corrected_raw [ : : - 1 ] ) [ : : - 1 ] del pvals_corrected_raw pvals_corrected [ pvals_corrected > 1 ] = 1 pvals_corrected_ = np . empty_like ( pvals_corrected ) pvals_corrected_ [ pvals_sortind ] = pvals_corrected del pvals_corrected reject_ = np . empty_like ( reject ) reject_ [ pvals_sortind ] = reject return reject_ , pvals_corrected_
benjamini hocheberg fdr correction. inspired by statsmodels
benjamini hocheberg fdr correction . inspired by statsmodels