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Hypothesis prioritisation multi-trait colocalization
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Christopher Foley
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README.md

HyPrColoc

Hypothesis Prioritisation in multi-trait Colocalization (HyPrColoc) analyses.

Functions

  • hyprcoloc - performs multi-trait colocalization across multiple traits.

Installation

  1. install.packages("devtools")
  2. library(devtools)
  3. install_github("jrs95/hyprcoloc", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE)
  4. library(hyprcoloc)
  5. browseVignettes("hyprcoloc")

Example

# Regression coefficients and standard errors from ten GWAS studies (Traits 1-5, 6-8 & 9-10 colocalize)
betas <- hyprcoloc::test.betas
head(betas)
ses <- hyprcoloc::test.ses
head(ses)

# Trait names and SNP IDs
traits <- paste0("T", 1:10)
rsid <- rownames(betas)

# Colocalization analysis
hyprcoloc(betas, ses, trait.names=traits, snp.id=rsid)

Citations

  • HyPrColoc: Foley CN, Staley JR, et al. A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. BioRxiv 2019. doi: https://doi.org/10.1101/592238
  • LD blocks: Berisa T & Pickrell JK. Approximately independent linkage disequilibrium blocks in human populations. Bioinformatics 2016; 32(2):283-285
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