def positioning(self, wig, rd=None):
'''
Description:
Calculate nucleosome (summit) positioning score and P value.
Parameter:
wig: a Wig class instance containing nucleosome occupancy data
rd: the half size of the region flanking each summit used to calculate nucleosome fuzziness
Value:
None
'''
from rpy2.robjects import r, FloatVector
from random import shuffle
from functions import log10fuztest
#ct=r('''function(x){return(chisq.test(x)$p.value)}''')
#xx=numpy.array(range(rd*2))
#ftest=r('''function(x,y){return(var.test(x,y)$p.value)}''')
smt = self
step = wig.step
#rd=rd/step+1
#tarray=numpy.array(0.0)
#tarray.resize(rd*2,refcheck=0)
for cr in smt.data:
print cr
ps = smt.data[cr]['p']
s, ppos = numpy.array([0.0] * rd * 2), numpy.array([0.0] * rd * 2)
lth = ps.size
s.resize(lth, refcheck=0)
ppos.resize(lth, refcheck=0)
if wig.data.has_key(cr): #add by kaifu on Jan 27, 2014
w = wig.data[cr]
i = 0
while (i < lth):
temp = log10fuztest(pc=ps[i],
pt=ps[i],
cr=cr,
cwig=wig,
twig=None,
rd=rd)
ppos[i], s[i] = temp
i += 1
smt.data[cr]['s'] = s
smt.data[cr]['ppos'] = ppos
def positioning(self,wig,rd=None):
'''
Description:
Calculate nucleosome (summit) positioning score and P value.
Parameter:
wig: a Wig class instance containing nucleosome occupancy data
rd: the half size of the region flanking each summit used to calculate nucleosome fuzziness
Value:
None
'''
from rpy2.robjects import r, FloatVector
from random import shuffle
from functions import log10fuztest
#ct=r('''function(x){return(chisq.test(x)$p.value)}''')
#xx=numpy.array(range(rd*2))
#ftest=r('''function(x,y){return(var.test(x,y)$p.value)}''')
smt=self
step=wig.step
#rd=rd/step+1
#tarray=numpy.array(0.0)
#tarray.resize(rd*2,refcheck=0)
for cr in smt.data:
print cr
ps=smt.data[cr]['p']
s,ppos=numpy.array([0.0]*rd*2),numpy.array([0.0]*rd*2)
lth=ps.size
s.resize(lth,refcheck=0)
ppos.resize(lth,refcheck=0)
if wig.data.has_key(cr):#add by kaifu on Jan 27, 2014
w=wig.data[cr]
i=0
while(i<lth):
temp=log10fuztest(pc=ps[i],pt=ps[i],cr=cr,cwig=wig,twig=None,rd=rd)
ppos[i],s[i]=temp
i+=1
smt.data[cr]['s']=s
smt.data[cr]['ppos']=ppos