def get_hic_zscores(self, normalized=True, zscored=True):
"""
Computes a normalization of Hi-C raw data. Result will be stored into
the private Experiment._zscore list
:param True normalized: whether to normalize the result using the
weights (see :func:`normalize_hic`)
:param True zscored: apply a z-score transform over the data.
"""
values = []
if normalized:
for i in xrange(self.size):
# zeros are rows or columns having a zero in the diagonal
if i in self._zeros:
continue
for j in xrange(self.size):
if j in self._zeros:
continue
try:
values.append(
self.hic_data[0][i * self.size + j] /\
self.wght[0][i * self.size + j])
except ZeroDivisionError:
values.append(0.0)
else:
for i in xrange(self.size):
if i in self._zeros:
continue
for j in xrange(self.size):
if j in self._zeros:
continue
values.append(self.hic_data[0][i * self.size + j])
# compute Z-score
if zscored:
zscore(values, self.size)
iterval = values.__iter__()
for i in xrange(self.size):
if i in self._zeros:
continue
for j in xrange(self.size):
if j in self._zeros:
continue
zsc = iterval.next()
self._zscores.setdefault(i, {})
self._zscores[i][j] = zsc
self._zscores.setdefault(j, {})
self._zscores[j][i] = zsc
def to_binary(exp, method='bin'):
exp.normalize_hic(method='bytot')
hic = exp.hic_data[0][:]
nhic = [(float(hic[i]) / exp.wght[0][i]) if exp.wght[0][i] else 0.0 \
for i in xrange(exp.size**2)]
zscore(nhic, exp.size)
if method == 'trin':
return [1 if z.__str__() == 'nan' \
else 0 if -1 < z < 1 else 1 if z > 0 else -1 for z in nhic]
elif method == 'fivn':
return [1 if z.__str__() == 'nan' \
else 0 if z < -2 \
else 1 if z < -1 \
else 2 if z < 1 \
else 3 if z < 2 \
else 4 for z in nhic]
return [0 if z < 0 else 1 for z in nhic]
def to_binary(exp, method='bin'):
exp.normalize_hic(method='bytot')
hic = exp.hic_data[0][:]
nhic = [(float(hic[i]) / exp.wght[0][i]) if exp.wght[0][i] else 0.0 \
for i in xrange(exp.size**2)]
zscore(nhic, exp.size)
if method == 'trin':
return [1 if z.__str__() == 'nan' \
else 0 if -1 < z < 1 else 1 if z > 0 else -1 for z in nhic]
elif method == 'fivn':
return [1 if z.__str__() == 'nan' \
else 0 if z < -2 \
else 1 if z < -1 \
else 2 if z < 1 \
else 3 if z < 2 \
else 4 for z in nhic]
return [0 if z < 0 else 1 for z in nhic]
