runsusie: Run susie on a single coloc-structured dataset

In coloc: Colocalisation Tests of Two Genetic Traits

Run susie on a single coloc-structured dataset

Description

run susie_rss storing some additional information for coloc

Usage

runsusie(
  d,
  suffix = 1,
  maxit = 100,
  repeat_until_convergence = TRUE,
  s_init = NULL,
  ...
)

Arguments

d	coloc dataset, must include LD (signed correlation matrix) and N (sample size)
suffix	suffix label that will be printed with any error messages
maxit	maximum number of iterations for the first run of susie_rss(). If susie_rss() does not report convergence, runs will be extended assuming repeat_until_convergence=TRUE. Most users will not need to change this default.
repeat_until_convergence	keep running until susie_rss() indicates convergence. Default TRUE. If FALSE, susie_rss() will run with maxit iterations, and if not converged, runsusie() will error. Most users will not need to change this default.
s_init	used internally to extend runs that haven't converged. don't use.
...	arguments passed to susie_rss. In particular, if you want to match some coloc defaults, set prior_variance=0.2^2 (if a case-control trait) or (0.15/sd(Y))^2 if a quantitative trait estimate_prior_variance=FALSE otherwise susie_rss will estimate the prior variance itself

Value

results of a susie_rss run, with some added dimnames

Author(s)

Chris Wallace

Examples

library(coloc)
data(coloc_test_data)
result=runsusie(coloc_test_data$D1)
summary(result)

coloc documentation built on Oct. 3, 2023, 5:07 p.m.