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"""
DESCRIPTION:
TODO: Add a description for the module
FUNCTIONS:
compute_correlation:
TODO: Describe what the function does..."""
from scipy import stats
## From GN1: mostly for clustering and heatmap generation
def __items_with_values(dbdata, userdata):
"""Retains only corresponding items in the data items that are not `None` values.
This should probably be renamed to something sensible"""
filtered = [x for x in zip(dbdata, userdata) if x[0] is not None and x[1] is not None]
return tuple(zip(*filtered)) if filtered else ([], [])
def compute_correlation(dbdata, userdata):
"""Compute the Pearson correlation coefficient.
This is extracted from
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/webqtlUtil.py#L622-L647
"""
x_items, y_items = __items_with_values(dbdata, userdata)
correlation = stats.pearsonr(x_items, y_items)[0] if len(x_items) >= 6 else 0
return (correlation, len(x_items))
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