Samples from the posterior distribution
posterior_samples.Rd
Samples from the posterior distribution
Usage
posterior_samples(
beta,
se,
eaf,
R,
maxsize,
tau0,
r0,
niter,
burnin,
p,
seed = 456,
excl.burnin = TRUE,
a0 = 1,
b0 = NULL,
inds0 = NULL,
standardize = TRUE,
verbose = TRUE,
clump = TRUE,
clump_r2 = 0.99^2,
check_ld = FALSE,
ala = NULL
)
Arguments
- beta
Vector of effect sizes.
- se
Vector of standard errors.
- eaf
Vector of effect allele frequencies.
- R
LD matrix.
- maxsize
The maximum number of causal variants.
- tau0
Parameter tau.
- r0
Parameter $r$.
- niter
Number of iterations.
- burnin
Number of burn-in samples.
- p
Number of variants.
- seed
Random seed.
- excl.burnin
Should the burn-in be excluded?
- a0
Hyperparameter a for the model size prior.
- b0
Hyperparameter b for the model size prior.
- inds0
Initial model indices (not used).
- standardize
Should the effect sizes be standardised? Defaults to TRUE.
- verbose
Verbose output.
- clump
Whether to clump extremely highly correlated variants.
- clump_r2
Clumping threshold for extremely highly correlated variants.
- check_ld
Should the Z-scores be checked for LD discrepancy?
- ala
Whether Approximate Laplace should be used?