compute_shrinkage_metrics: This function computes various shrinkage metrics...

In ollyburren/cupcake: PCA for GWAS

Description

This function computes various shrinkage metrics compute_shrinkage_metrics computes various shrinkage metrics

Usage

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.

ollyburren/cupcake documentation built on July 30, 2020, 9:58 a.m.