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hint

CRAN status metacran downloads R build status

Summary

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.

Installation

install.packages("hint")

Usage

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)  =  0.1596769

References

Kalinka (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.
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