This function computes various shrinkage metrics compute_shrinkage_metrics computes various shrinkage metrics

This function computes various shrinkage metrics compute_shrinkage_metrics computes various shrinkage metrics

compute_shrinkage_metrics(DT, pi_i = 1e-04)

Arguments

DT

data.table object for basis traits as returned by get_gwas_data
pi_i

numeric the prior probability that a variant is causal see ws_shrinkage

Value

a data.table object.

  1. pid - unique id using chr and position (useful for merging back)

  2. bshrink - Bayesian shrinkage based on association across all basis traits

  3. emp_maf_se - empirically derived standard error for MAF

  4. est_maf_se - estimated standard error for MAF

  5. emp_shrinkage - overall shrinkage using emp_maf_se

  6. est_shrinkage - overall shrinkage using est_maf_se

see also maf_se_estimate_sample_size.