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coloc

Repo for the R package coloc

https://github.com/chr1swallace/coloc

Science Score: 59.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov, wiley.com, plos.org
  • ✓
    Committers with academic emails
    3 of 5 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Repo for the R package coloc

Basic Info
  • Host: GitHub
  • Owner: chr1swallace
  • Language: R
  • Default Branch: main
  • Size: 48.1 MB
Statistics
  • Stars: 171
  • Watchers: 4
  • Forks: 46
  • Open Issues: 62
  • Releases: 0
Created almost 13 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog

README.md

coloc

CRAN_Status_Badge

The coloc package can be used to perform genetic colocalisation analysis of two potentially related phenotypes, to ask whether they share common genetic causal variant(s) in a given region.

Most of the questions I get relate to misunderstanding the assumptions behind coloc (dense genotypes across a single genomic region) and/or the data structures used. Please read vignette("a02_data",package="coloc") before starting an issue. The FAQ page may also be helpful.

Installation

To install the latest stable CRAN version of coloc run:

R install.packages("coloc")

To install the development version of coloc from GitHub run:

R if(!require("remotes")) install.packages("remotes") # if necessary remotes::install_github("chr1swallace/coloc@main",build_vignettes=TRUE)

Version 6

This update (version 6) adds the ability to use variant-specific priors in coloc. See

  • Pullin JM, Wallace C (2025) Variant-specific priors clarify colocalisation analysis. PLoS Genet 21(5): e1011697. https://doi.org/10.1371/journal.pgen.1011697

for a description of the implementation and a comparison of different sources of prior information. If you use variant-specific priors in coloc please cite this paper.

More detail is also available in the vignette a07variantspecific_priors.html accessible by

R vignette("a07-variant_specific_priors",package="coloc")

Version 5

Version 5 superseded previously published version 4 by introducing use of the SuSiE approach to deal with multiple causal variants rather than conditioning or masking. See

  • Wang, G., Sarkar, A., Carbonetto, P., & Stephens, M. (2020). A simple new approach to variable selection in regression, with application to genetic fine mapping. Journal of the Royal Statistical Society: Series B (Statistical Methodology). https://doi.org/10.1111/rssb.12388

for the full SuSiE paper and

  • Wallace (2021). A more accurate method for colocalisation analysis allowing for multiple causal variants. PLoS Genetics. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009440

for a description of its use in coloc.

Note that in all simulations, susie outperforms the earlier conditioning approach, so is recommended. To use susie with coloc please look at coloc.susie. It can take raw datasets, but the time consuming part is running SuSiE. coloc runs SuSiE and saves a little extra information using the runsusie function before running an adapted colocalisation on the results. So please look at the docs for runsusie too. A helpful recipe is

  1. Run runsusie on dataset 1, storing the results
  2. Run runsusie on dataset 2, storing the results
  3. Run coloc.susie on the two outputs from above

More detail is available in the vignette a06_SuSiE.html accessible by

R vignette("a06_SuSiE",package="coloc")

Frequently Asked Questions

Please see the FAQ page if you have issues or questions.

Background reading

For usage, please see the vignette at https://chr1swallace.github.io/coloc

Key previous references are:

Owner

  • Name: Chris Wallace
  • Login: chr1swallace
  • Kind: user
  • Location: Cambridge, UK
  • Company: University of Cambridge

Statisitician using genomics to understand immune-mediated diseases. Github hosts mainly R packages to do statistical analysis of genetic data.

GitHub Events

Total
  • Issues event: 12
  • Watch event: 24
  • Issue comment event: 31
  • Push event: 7
  • Pull request event: 9
  • Fork event: 3
  • Create event: 2
Last Year
  • Issues event: 12
  • Watch event: 24
  • Issue comment event: 31
  • Push event: 7
  • Pull request event: 9
  • Fork event: 3
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 291
  • Total Committers: 5
  • Avg Commits per committer: 58.2
  • Development Distribution Score (DDS): 0.258
Past Year
  • Commits: 12
  • Committers: 1
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
chr1swallace c****4@c****k 216
chr1swallace c****e@c****k 67
John Blischak j****k@g****m 3
Vincent Plagnol v****l@g****m 3
Hui-Guo h****3@c****k 2
Committer Domains (Top 20 + Academic)
cam.ac.uk: 2 cimr.cam.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 146
  • Total pull requests: 29
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 116
  • Total pull request authors: 11
  • Average comments per issue: 3.57
  • Average comments per pull request: 0.79
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 16
  • Pull requests: 10
  • Average time to close issues: about 1 hour
  • Average time to close pull requests: 1 day
  • Issue authors: 14
  • Pull request authors: 3
  • Average comments per issue: 1.56
  • Average comments per pull request: 0.6
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Zepeng-Mu (7)
  • zillurbmb51 (5)
  • JFF1594032292 (4)
  • mocksu (4)
  • schavezchavez (3)
  • HKJ396 (3)
  • oborisov (3)
  • Filago4 (2)
  • shannjiang (2)
  • maegsul (2)
  • MoMaz123 (2)
  • jielab (2)
  • zhuxxyy12 (2)
  • nshrine (2)
  • maguileraf (2)
Pull Request Authors
  • jeffreypullin (11)
  • chr1swallace (6)
  • GRealesM (5)
  • twillis209 (4)
  • pc494 (3)
  • ramin777777 (2)
  • cfbeuchel (2)
  • jdblischak (2)
  • olivroy (2)
  • fromOmelas (1)
  • Joannavonberg (1)
Top Labels
Issue Labels
enhancement (3) bug (2)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 1,390 last-month
  • Total docker downloads: 79
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 12
    (may contain duplicates)
  • Total versions: 19
  • Total maintainers: 1
proxy.golang.org: github.com/chr1swallace/coloc
  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
cran.r-project.org: coloc

Colocalisation Tests of Two Genetic Traits

  • Versions: 16
  • Dependent Packages: 3
  • Dependent Repositories: 12
  • Downloads: 1,390 Last month
  • Docker Downloads: 79
Rankings
Forks count: 2.0%
Stargazers count: 3.7%
Average: 7.7%
Dependent repos count: 8.3%
Downloads: 10.7%
Dependent packages count: 13.7%
Maintainers (1)
cew54@cam.ac.uk
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • data.table * imports
  • ggplot2 * imports
  • grDevices * imports
  • methods * imports
  • stats * imports
  • susieR >= 0.12.06 imports
  • utils * imports
  • viridis * imports
  • knitr * suggests
  • magrittr * suggests
  • mvtnorm * suggests
  • rmarkdown * suggests
  • snpStats * suggests
  • testthat * suggests