Commit 88cea0dd authored by Blaise Li's avatar Blaise Li
Browse files

More documentation.

parent a872a0e1
......@@ -105,10 +105,14 @@ def do_deseq2(cond_names, conditions, counts_data,
def median_ratio_to_pseudo_ref_size_factors(counts_data):
"""Adapted from DESeq paper (doi:10.1186/gb-2010-11-10-r106)"""
"""Adapted from DESeq paper (doi:10.1186/gb-2010-11-10-r106)
All libraries are used to define a pseudo-reference, which has
the geometric mean across libraries for a given gene in *counts_data*.
For a given library, the median across genes of the ratios to the
pseudo-reference is used as size factor."""
# Add pseudo-count to compute the geometric mean, then remove it
#pseudo_ref = (counts_data + 1).apply(gmean, axis=1) - 1
# Ignore lines with zeroes instead:
# Ignore lines with zeroes instead (may be bad for IP: many zeroes expected):
pseudo_ref = (counts_data[ > 0]).apply(gmean, axis=1)
def median_ratio_to_pseudo_ref(col):
return (col / pseudo_ref).median()
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