I want to calculate p-value in python using R.I am using this package rpy2.I am generating count_a and count_b on the fly,and calculate p-values along with it. When I run my script,python closes unexpectedly,and get this error message:
"Error: 'rho' must be an environment not NULL: detected in C-level eval During startup - Warning message:
Abort trap: 6"
The data is below:
count_a count_b 94 107 109 92 90 89 18 13
Below is my code:
import rpy2.robjects as R out= open(args.outfile, 'w') binom=R.r['binom.test'](c(count_a,count_b)) P_val=binom['p.value'] out.write(str(count_a) + '\t' + str(count_b) + '\t' + str(P_val) out.close()
Any suggestions,or options to calculate p-value in python on a pair of values?
binom object is calculated:
Exact binomial test
data: c(94L, 107L) number of successes = 94, number of trials = 201, p-value = 0.3974
alternative hypothesis: true probability of success is not equal to 0.5 95 percent confidence interval: 0.3971286 0.5391627
probability of success
However while extracting the p-value,I am getting this error:
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/robjects/vectors.py", line 233, in getitem res = super(Vector, self).getitem(i) TypeError: 'str' object cannot be interpreted as an index