analytically compute the variance of a projection given a standard error of beta for a given trait compute_seb_proj_var

compute_seb_proj_var(gwas.DT, shrink.DT, man.DT, w.DT, ref_gt_dir,
  method = "shrinkage", quiet = FALSE)

Arguments

gwas.DT

a data.table - variants and summary statistics

shrink.DT

a data.table - as returned by compute_shrinkage_metrics

man.DT

a data.table - snp manifest file that maps snps to ld.block

w.DT

a data.table - a data table of weights/rotations from a basis first column is 'pid' and subsequent columns for each principal component.

ref_gt_dir

scalar - path to a dir of R objects named CHR_1kg.RData containing reference GT in snpMatrix format

method

scalar - shrinkage method to use (default shrinkage) but also valid is none

quiet

a scalar - boolean whether to show progress messages

Value

a scalar of variances for each principal component