binomTest(y1, y2, n1=sum(y1), n2=sum(y2), p=n1/(n1+n2))
y1
.
Non-integer values are rounded to the nearest integer.p
is supplied.p
is supplied.y1
to the total for each gene under the null hypothesis.n1/(n1+n2)
.
The two-sided rejection region is chosen analogously to Fisher's test.
Specifically, the rejection region consists of those values with smallest probabilities
under the null hypothesis.
When the counts are reasonably large, the binomial test, Fisher's test and Pearson's chisquare all give the same results.
When the counts are smaller, the binomial test is usually to be preferred in this context.
This function replaces the earlier sage.test
functions in the statmod and sagenhaft packages.
It produces the same results as binom.test
in the stats packge, but is much faster.sage.test
(statmod package), binom.test
(stats package)binomTest(c(0,5,10),c(0,30,50),n1=10000,n2=15000)
# Univariate equivalents:
binom.test(5,5+30,p=10000/(10000+15000))$p.value
binom.test(10,10+50,p=10000/(10000+15000))$p.value
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