analytically compute the variance of a projection given a standard error of beta for a given trait for sparse basis compute_seb_proj_var_sparse

compute_seb_proj_var_sparse(gwas.DT, shrink.DT, w.DT, sm,
  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

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.

sm

snpMatrix object - a snp matrix object of reference genotypes for

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