moloc_test: moloc_test

In clagiamba/moloc: Multiple Traits Co-localization

Description

Bayesian multiple trait colocalization analysis using list of data.frames

Usage

moloc_test(listData, prior_var = c(0.01, 0.1, 0.5), priors = c(1e-04, 1e-06,
  1e-07), save.SNP.info = FALSE)

Arguments

listData	A list of data frames to be analyzed. Each data frame must contain columns named SNP (the SNP name consistent across all the data frames), BETA, SE
prior_var	One or more numbers for the prior variance of the ABF.
priors	are numbers, the prior for one variant to be associated with 1 trait and with each additional trait
compute_sdY	Estimate standard deviation of Y. If false assume sdY is 1
...	parameters passed to adjust_bfs, config_coloc, snp_ppa

Details

Runs adjust_bfs, config_coloc, snp_ppa

Value

A list of three elements: First is a data frame with 4 variables: priors ('prior'), likelihoods ('sumbf') and posteriors ('loglkl' and 'PPA') for each configuration; Second is a number, the number of SNPs in common in the region; Third is a data frame with 2 variables: SNP with the best posterior for each scenario ('coloc_ppas'), SNP name with the best posterior for each scenario ('best.snp.coloc').

Author(s)

Claudia Giambartolomei

Claudia Giambartolomei

Examples

moloc <- moloc_test(listData) # uses default priors

clagiamba/moloc documentation built on Jan. 25, 2021, 2:43 a.m.