binomTest
in the edgeR Bioconductor package and
is no longer updated.
It may be removed in a later release of this package.
Computes p-values for differential abundance for each tag between two digital libraries,
conditioning on the total count for each tag.
The counts in each group as a proportion of the whole are assumed to follow a binomial distribution.sage.test(x, y, n1=sum(x), n2=sum(y))
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 is a later version of the earlier sage.test
function in the sagenhaft Bioconductor package.
This function has been replaced by binomTest
in the edgeR package.binomTest
(edgeR package), binom.test
(stats package)sage.test(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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