Package: coloc 6.0.0

coloc: Colocalisation Tests of Two Genetic Traits

Performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>, Pullin and Wallace (2025) <doi:10.1101/2024.08.21.608957>.

Authors:Chris Wallace [aut, cre], Claudia Giambartolomei [aut], Vincent Plagnol [ctb], Tom Willis [aut], Jeffrey Pullin [aut]

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coloc/json (API)
NEWS

# Install 'coloc' in R:

install.packages('coloc', repos = c('https://chr1swallace.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/chr1swallace/coloc/issues

Pkgdown site:https://chr1swallace.github.io

Datasets:

coloc_test_data - Simulated data to use in testing and vignettes in the coloc package
eqtlgen_density_data - EQTLGen estimated distance density

On CRAN:

12.68 score 164 stars 3 packages 916 scripts 2.4k downloads 49 mentions 21 exports 40 dependencies

Last updated 4 days agofrom:cfd4800a77. Checks:1 OK, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 27 2025
R-4.5-win	WARNING	Mar 27 2025
R-4.5-mac	WARNING	Mar 27 2025
R-4.5-linux	WARNING	Mar 27 2025
R-4.4-win	WARNING	Mar 27 2025
R-4.4-mac	WARNING	Mar 27 2025
R-4.4-linux	WARNING	Mar 27 2025
R-4.3-win	WARNING	Mar 27 2025
R-4.3-mac	WARNING	Mar 27 2025

Exports:annotate_susie check_alignment check_dataset check.alignment check.dataset coloc.abf coloc.bf_bf coloc.signals coloc.susie coloc.susie_bf credible.sets findends finemap.abf finemap.bf finemap.signals plot_dataset plot_extended_dataset process.dataset runsusie sensitivity subset_dataset

Dependencies:cli colorspace crayon data.table fansi farver ggplot2 glue gridExtra gtable irlba isoband labeling lattice lifecycle magrittr MASS Matrix matrixStats mgcv mixsqp munsell nlme pillar pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo reshape rlang scales susieR tibble utf8 vctrs viridis viridisLite withr

Coloc: a package for colocalisation analyses

Chris Wallace

Rendered froma01_intro.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2023-05-12
Started: 2019-07-08

Coloc: data structures

Chris Wallace

Rendered froma02_data.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2023-05-12
Started: 2021-03-23

Coloc: sensitivity to prior values

Chris Wallace

Rendered froma04_sensitivity.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2021-06-08
Started: 2019-07-08

Coloc: under a single causal variant assumption

Chris Wallace

Rendered froma03_enumeration.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2021-06-08
Started: 2019-07-08

Coloc: using SuSiE to relax the single causal variant assumption

Chris Wallace

Rendered froma06_SuSiE.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2022-05-05
Started: 2021-03-22

Coloc: using variant-specific priros in coloc

Jeffrey Pullin

Rendered froma07_variant-specific-priors.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2025-03-27
Started: 2025-03-27

DEPRECATED Coloc: relaxing the single causal variant assumption

Chris Wallace

Rendered froma05_conditioning.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2022-03-21
Started: 2019-07-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Colocalisation tests of two genetic traits	-package coloc-package
annotate susie_rss output for use with coloc_susie	annotate_susie
Internal function, approx.bf.estimates	approx.bf.estimates
Internal function, approx.bf.p	approx.bf.p
binomial to linear regression conversion	bin2lin
check alignment	check.alignment check_alignment
check_dataset	check.dataset check_dataset
Simulated data to use in testing and vignettes in the coloc package	coloc_test_data
Fully Bayesian colocalisation analysis using Bayes Factors	coloc.abf
Coloc data through Bayes factors	coloc.bf_bf
Bayesian colocalisation analysis with detailed output	coloc.detail
Post process a coloc.details result using masking	coloc.process
Coloc with multiple signals per trait	coloc.signals
run coloc using susie to detect separate signals	coloc.susie
run coloc using susie to detect separate signals	coloc.susie_bf
combine.abf	combine.abf
credible.sets	credible.sets
eQTLGen estimated distance density	eqtlgen_density_data
generate conditional summary stats	est_cond
estgeno1	estgeno.1.cse estgeno.1.ctl
Pick out snp with most extreme Z score	find.best.signal
trim a dataset to central peak(s)	findends
trim a dataset to only peak(s)	findpeaks
Bayesian finemapping analysis	finemap.abf
Finemap data through Bayes factors	finemap.bf
Finemap multiple signals in a single dataset	finemap.signals
logbf 2 pp	logbf_to_pp
logdiff	logdiff
logsum	logsum
find the next most significant SNP, conditioning on a list of sigsnps	map_cond
find the next most significant SNP, masking a list of sigsnps	map_mask
plot a coloc dataset	plot_dataset
Draw extended plot of summary statistics for two coloc datasets	plot_extended_dataset
plot a coloc_abf object	plot.coloc_abf
print.coloc_abf	print.coloc_abf
process.dataset	process.dataset
Run susie on a single coloc-structured dataset	runsusie
Estimate trait variance, internal function	sdY.est
Prior sensitivity for coloc	sensitivity
subset_dataset	subset_dataset
Var.data	Var.data
Var.data	Var.data.cc

Package: coloc 6.0.0

coloc: Colocalisation Tests of Two Genetic Traits

Coloc: a package for colocalisation analyses

Coloc: data structures

Coloc: sensitivity to prior values

Coloc: under a single causal variant assumption

Coloc: using SuSiE to relax the single causal variant assumption

Coloc: using variant-specific priros in coloc

DEPRECATED Coloc: relaxing the single causal variant assumption

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)