Estimates cTWAS parameters using EM
est_param(
region_data,
init_group_prior = NULL,
init_group_prior_var = NULL,
group_prior_var_structure = c("shared_type", "shared_context", "shared_nonSNP",
"shared_all", "independent"),
niter_prefit = 3,
niter = 30,
min_p_single_effect = 0.8,
use_null_weight = TRUE,
min_var = 2,
min_gene = 1,
min_group_size = 100,
ncore = 1,
logfile = NULL,
verbose = FALSE,
...
)a list object indexing regions, variants and genes.
a vector of initial values of prior inclusion probabilities for SNPs and genes.
a vector of initial values of prior variances for SNPs and gene effects.
a string indicating the structure to put on the prior variance parameters. "shared_type" allows all groups in one molecular QTL type to share the same variance parameter. "shared_context" allows all groups in one context (tissue, cell type, condition) to share the same variance parameter. "shared_nonSNP" allows all non-SNP groups to share the same variance parameter. "shared_all" allows all groups to share the same variance parameter. "independent" allows all groups to have their own separate variance parameters.
the number of iterations of the E-M algorithm to perform during the initial parameter estimation step.
the number of iterations of the E-M algorithm to perform during the complete parameter estimation step.
Regions with probability greater than min_p_single_effect of
having at most one causal effect will be used selected for the complete parameter estimation step.
If TRUE, allow for a probability of no effect in susie.
minimum number of variables (SNPs and genes) in a region.
minimum number of genes in a region.
Minimum number of variables in a group.
The number of cores used to parallelize computation over regions.
The log filename. If NULL, print log info on screen.
If TRUE, print detail messages.
Additional arguments of susie_rss.
a list with estimated parameters