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hint is an R package for performing
hypothesis testing based on Hypergeometric Intersection distributions.
For example if you had three gene sets arising from three separate
experiments with x genes shared between the three, you
could determine the probability of arriving at this intersection size by
chance. See the companion paper for more
information.
install.packages("hint")library(hint)
## The probability of an intersection of size 5 or greater
## when sampling 15, 8, and 7 balls from three urns
## each with 1 ball in each of 29 categories.
phint(29, c(15, 8, 7), vals = 5)
v cum.p
1 5 0.0002289938
## Formalising a hypothesis test using 'hint.test'.
# Categories given in the first column.
# Numbers of balls in each category given in subsequent columns: each column representing an urn.
dd <- data.frame(categories = letters[1:20],
urn1_count = rep(1,20),
urn2_count = rep(1,20))
tt <- hint.test(dd, letters[1:9],
letters[4:15], alternative = "greater")
print(tt)
Hypergeometric intersection test
Parameters:
n a b q v
20 9 12 0 6
P(X >= v) = 0.4649917
plot(tt)
## Allow duplicates in the second urn.
dd <- data.frame(letters[1:20],
rep(1,20),
c(rep(1,4), rep(2,16)))
tt <- hint.test(dd, letters[1:9],
letters[9:14], alternative = "less")
print(tt)
Hypergeometric intersection test
Parameters:
n a b q v
20 9 6 16 1
P(X <= v) = 0.1596769Kalinka (2013). The probability of drawing intersections: extending the hypergeometric distribution. arXiv.1305.0717
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.