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Run susie on a single coloc-structured dataset

Source: R/susie.R
runsusie.Rd

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

Chris Wallace

Examples

library(coloc)
data(coloc_test_data)
result=runsusie(coloc_test_data$D1)
#> running max iterations: 100
#> 	converged: TRUE
summary(result)
#> 
#> Variables in credible sets:
#> 
#>  variable variable_prob cs
#>       105     0.9593968  1
#> 
#> Credible sets summary:
#> 
#>  cs cs_log10bf cs_avg_r2 cs_min_r2 variable
#>   1    10.2121         1         1      105