def preprocess(self):
matplotlib.use("Agg")
gs = GenomicSubset(self.params.region)
A = SnpSubset(self.refpanel, bedtool=gs.bedtool)
W = A.expanded_by(self.params.ld_window / 1000.0)
R = BlockDiag.ld_matrix(self.refpanel, W.irs.ranges(), 300, band_units="SNPs")
pickle.dump(R, self.R_file(mode="wb"), 2)
# R.plot(A.irs, filename=self.R_plotfilename())
RA = R.zero_outside_irs(A.irs)
pickle.dump(RA, self.RA_file(mode="wb"), 2)
def preprocess(self):
matplotlib.use('Agg')
gs = GenomicSubset(self.params.region)
ss = SnpSubset(self.refpanel, bedtool=gs.bedtool)
RA = BlockDiag.ld_matrix(self.refpanel, ss.irs.ranges(), self.params.ld_bandwidth / 1000.)
try: # if the plotting has some error we don't want to not save the stuff
# RA.plot(ss.irs, filename=self.RA_plotfilename())
pass
except:
pass
pickle.dump(RA, self.RA_file(mode='wb'), 2)
def preprocess(self):
matplotlib.use('Agg')
gs = GenomicSubset(self.params.region)
ss = SnpSubset(self.refpanel, bedtool=gs.bedtool)
RA = BlockDiag.ld_matrix(self.refpanel, ss.irs.ranges(),
self.params.ld_bandwidth / 1000.)
try: # if the plotting has some error we don't want to not save the stuff
# RA.plot(ss.irs, filename=self.RA_plotfilename())
pass
except:
pass
pickle.dump(RA, self.RA_file(mode='wb'), 2)
def preprocess(self):
matplotlib.use('Agg')
gs = GenomicSubset(self.params.region)
A = SnpSubset(self.refpanel, bedtool=gs.bedtool)
W = A.expanded_by(self.params.ld_window / 1000.)
R = BlockDiag.ld_matrix(self.refpanel,
W.irs.ranges(),
300,
band_units='SNPs')
pickle.dump(R, self.R_file(mode='wb'), 2)
# R.plot(A.irs, filename=self.R_plotfilename())
RA = R.zero_outside_irs(A.irs)
pickle.dump(RA, self.RA_file(mode='wb'), 2)
def preprocess(self):
matplotlib.use("Agg")
gs = GenomicSubset(self.params.region)
A = SnpSubset(self.refpanel, bedtool=gs.bedtool)
W = self.window(A)
R = BlockDiag.ld_matrix(self.refpanel, W.irs.ranges(), 1000000) # bandwidth=infty
pickle.dump(R, self.R_file(mode="wb"), 2)
try: # if the plotting has some error we don't want to not save the stuff
# R.plot(A.irs, filename=self.R_plotfilename())
pass
except:
pass
RA = R.zero_outside_irs(A.irs)
pickle.dump(RA, self.RA_file(mode="wb"), 2)
def preprocess(self):
matplotlib.use('Agg')
gs = GenomicSubset(self.params.region)
A = SnpSubset(self.refpanel, bedtool=gs.bedtool)
W = self.window(A)
R = BlockDiag.ld_matrix(self.refpanel, W.irs.ranges(),
1000000) # bandwidth=infty
pickle.dump(R, self.R_file(mode='wb'), 2)
try: # if the plotting has some error we don't want to not save the stuff
# R.plot(A.irs, filename=self.R_plotfilename())
pass
except:
pass
RA = R.zero_outside_irs(A.irs)
pickle.dump(RA, self.RA_file(mode='wb'), 2)