def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
changepts = []
for n in self.G.nodes_iter():
expr_data = self.get_expr_data(*n)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug('%s changepoint node=(%s-%s) '
'pos=%d interval=(%d-%d) p=%.3f fc=%.3f' %
(str(self), n.start, n.end, cp.pos, cp.start,
cp.end, cp.pvalue, cp.foldchange))
return changepts
def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
changepts = []
for n in self.G.nodes_iter():
expr_data = self.get_expr_data(*n)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug('%s changepoint node=(%s-%s) '
'pos=%d interval=(%d-%d) p=%.3f fc=%.3f' %
(str(self), n.start,
n.end, cp.pos, cp.start, cp.end,
cp.pvalue, cp.foldchange))
return changepts
def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
changepts = []
for n_id in self.G:
n = self.get_node_interval(n_id)
expr_data = self.get_expr_data(n.start, n.end)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug(
'\t%s:%d-%d[%s] node: %s-%s cp:%d(%d-%d) '
'p=%.3f fc=%.3f' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), n.start, n.end, cp.pos,
cp.start, cp.end, cp.pvalue, cp.foldchange))
return changepts
def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
changepts = []
for n_id in self.G:
n = self.get_node_interval(n_id)
expr_data = self.get_expr_data(n.start, n.end)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug('\t%s:%d-%d[%s] node: %s-%s cp:%d(%d-%d) '
'p=%.3f fc=%.3f' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), n.start,
n.end, cp.pos, cp.start, cp.end,
cp.pvalue, cp.foldchange))
return changepts