Data

Tools

Indexes

Applications

Experiments

Open Source Science

hint

Tools for hypothesis testing based on Hypergeometric Intersection distributions

https://github.com/alextkalinka/hint

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: arxiv.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.9%) to scientific vocabulary

Keywords

combinatorics discrete-mathematics frequentist-statistics hypergeometric-distribution hypothesis-testing probability r-package
Last synced: 6 months ago · JSON representation

Repository

Tools for hypothesis testing based on Hypergeometric Intersection distributions

Basic Info
  • Host: GitHub
  • Owner: alextkalinka
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 65.4 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
combinatorics discrete-mathematics frequentist-statistics hypergeometric-distribution hypothesis-testing probability r-package
Created over 5 years ago · Last pushed about 4 years ago
Metadata Files
Readme

README.md

hint

CRAN status metacran downloads R build status <!-- badges: end -->

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

r install.packages("hint")

Usage

```r 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], urn1count = rep(1,20), urn2count = 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) ```

```r

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

Owner

  • Login: alextkalinka
  • Kind: user

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 10
  • Total Committers: 3
  • Avg Commits per committer: 3.333
  • Development Distribution Score (DDS): 0.5
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alex Kalinka a****a@c****k 5
Alex Kalinka A****a@c****k 4
alextkalinka 6****a 1
Committer Domains (Top 20 + Academic)
cancer.org.uk: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • alextkalinka (1)
  • alex-kalinka-cruk (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 228 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: hint

Tools for Hypothesis Testing Based on Hypergeometric Intersection Distributions

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 228 Last month
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Stargazers count: 35.2%
Dependent repos count: 35.5%
Average: 38.3%
Downloads: 62.3%
Maintainers (1)
alex.t.kalinka@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • grDevices * imports
  • graphics * imports
  • testthat >= 3.0.0 suggests